Query 037419
Match_columns 110
No_of_seqs 152 out of 1216
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 12:01:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037419.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037419hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.6 4.9E-15 1.1E-19 90.4 7.0 57 1-58 2-62 (62)
2 KOG1603 Copper chaperone [Inor 99.5 1.7E-13 3.7E-18 87.3 6.5 62 1-63 9-71 (73)
3 COG2608 CopZ Copper chaperone 99.4 1.7E-12 3.7E-17 82.4 7.4 58 4-62 10-70 (71)
4 KOG4656 Copper chaperone for s 99.1 1.2E-10 2.6E-15 88.1 6.6 65 2-67 12-76 (247)
5 PLN02957 copper, zinc superoxi 98.7 7E-08 1.5E-12 73.6 8.3 67 1-68 10-76 (238)
6 PRK10671 copA copper exporting 98.4 5.5E-07 1.2E-11 78.8 7.2 57 4-63 11-67 (834)
7 COG2217 ZntA Cation transport 98.2 4.8E-06 1E-10 72.4 6.5 56 4-61 10-69 (713)
8 TIGR00003 copper ion binding p 97.7 0.00032 7E-09 39.0 7.2 55 4-59 10-67 (68)
9 KOG0207 Cation transport ATPas 97.6 0.00012 2.5E-09 65.2 6.2 67 3-70 1-69 (951)
10 KOG0207 Cation transport ATPas 97.5 0.00024 5.2E-09 63.2 6.5 82 3-88 153-237 (951)
11 PRK10671 copA copper exporting 97.5 0.00027 5.9E-09 62.1 6.8 58 4-62 107-164 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.1 0.0013 2.8E-08 57.4 6.3 58 4-62 61-119 (741)
13 TIGR02052 MerP mercuric transp 94.4 0.56 1.2E-05 28.3 7.8 57 4-61 31-90 (92)
14 PRK13748 putative mercuric red 93.3 0.63 1.4E-05 38.8 8.4 60 4-64 8-69 (561)
15 cd00371 HMA Heavy-metal-associ 89.2 1.6 3.5E-05 21.3 6.8 48 4-51 6-55 (63)
16 COG1888 Uncharacterized protei 83.3 5.2 0.00011 26.9 5.5 48 14-62 24-79 (97)
17 PF02680 DUF211: Uncharacteriz 82.7 7.1 0.00015 26.3 6.0 50 13-63 21-78 (95)
18 PF01206 TusA: Sulfurtransfera 78.5 7.4 0.00016 23.5 4.8 52 3-62 6-57 (70)
19 PF01883 DUF59: Domain of unkn 75.9 2.5 5.4E-05 25.8 2.1 19 11-29 54-72 (72)
20 cd02410 archeal_CPSF_KH The ar 75.6 9.1 0.0002 27.6 5.2 60 11-70 55-120 (145)
21 PF13732 DUF4162: Domain of un 67.4 26 0.00057 21.5 6.1 44 17-63 25-70 (84)
22 PRK06418 transcription elongat 65.8 34 0.00073 25.1 6.5 64 1-64 10-98 (166)
23 PRK10553 assembly protein for 65.5 30 0.00065 22.6 5.6 29 11-39 19-47 (87)
24 PRK10509 bacterioferritin-asso 60.7 6.2 0.00013 24.3 1.6 20 1-20 33-52 (64)
25 cd03421 SirA_like_N SirA_like_ 58.1 38 0.00082 20.2 5.7 49 4-61 6-54 (67)
26 PF04972 BON: BON domain; Int 55.4 8.6 0.00019 22.6 1.5 31 12-43 2-35 (64)
27 cd04888 ACT_PheB-BS C-terminal 54.1 17 0.00037 21.6 2.8 20 10-29 55-74 (76)
28 PF08002 DUF1697: Protein of u 53.0 75 0.0016 22.1 6.3 50 12-62 22-75 (137)
29 PRK14054 methionine sulfoxide 52.6 36 0.00079 25.0 4.7 28 8-35 10-37 (172)
30 PF14437 MafB19-deam: MafB19-l 51.9 25 0.00054 25.4 3.7 32 6-38 110-142 (146)
31 TIGR02945 SUF_assoc FeS assemb 49.7 19 0.00041 23.3 2.6 21 12-32 58-78 (99)
32 TIGR03406 FeS_long_SufT probab 48.4 14 0.0003 27.2 2.0 20 12-31 134-153 (174)
33 PF09580 Spore_YhcN_YlaJ: Spor 48.4 35 0.00077 24.2 4.1 28 11-38 77-104 (177)
34 PF03927 NapD: NapD protein; 47.7 70 0.0015 20.2 5.7 40 11-51 17-57 (79)
35 PRK10555 aminoglycoside/multid 46.6 40 0.00088 30.9 5.0 42 11-52 159-208 (1037)
36 PRK09577 multidrug efflux prot 45.5 65 0.0014 29.6 6.1 46 11-57 158-211 (1032)
37 PRK11018 hypothetical protein; 45.2 75 0.0016 19.8 5.4 51 3-61 14-64 (78)
38 PF14492 EFG_II: Elongation Fa 43.2 60 0.0013 20.1 4.1 50 11-60 18-72 (75)
39 PRK05528 methionine sulfoxide 43.0 21 0.00045 25.8 2.2 28 8-35 8-35 (156)
40 PRK11023 outer membrane lipopr 42.6 63 0.0014 23.7 4.7 41 11-51 51-94 (191)
41 TIGR00489 aEF-1_beta translati 42.1 28 0.00061 22.9 2.5 21 11-31 64-84 (88)
42 TIGR03675 arCOG00543 arCOG0054 41.9 71 0.0015 27.9 5.6 61 10-70 71-137 (630)
43 TIGR03527 selenium_YedF seleni 41.8 1.1E+02 0.0025 22.6 6.0 51 4-62 5-55 (194)
44 PRK11023 outer membrane lipopr 40.9 94 0.002 22.8 5.4 40 10-49 128-169 (191)
45 PRK15127 multidrug efflux syst 40.8 58 0.0012 30.0 5.1 42 11-52 159-208 (1049)
46 PRK11200 grxA glutaredoxin 1; 40.2 45 0.00099 20.5 3.2 27 5-32 9-39 (85)
47 PF13193 AMP-binding_C: AMP-bi 39.0 37 0.00079 20.3 2.6 38 14-53 2-46 (73)
48 COG1094 Predicted RNA-binding 38.8 94 0.002 23.5 5.2 29 12-41 27-55 (194)
49 TIGR00915 2A0602 The (Largely 38.6 62 0.0013 29.8 4.9 42 11-52 159-208 (1044)
50 PF08210 APOBEC_N: APOBEC-like 38.5 49 0.0011 24.4 3.6 56 7-66 85-149 (188)
51 PF01625 PMSR: Peptide methion 37.5 38 0.00083 24.3 2.8 27 8-34 7-33 (155)
52 TIGR01676 GLDHase galactonolac 35.9 69 0.0015 27.7 4.5 39 18-59 110-148 (541)
53 PF04324 Fer2_BFD: BFD-like [2 35.7 11 0.00024 21.8 -0.2 19 2-20 35-53 (55)
54 PRK11198 LysM domain/BON super 35.7 95 0.0021 21.8 4.6 47 11-57 28-75 (147)
55 COG2151 PaaD Predicted metal-s 35.0 44 0.00096 22.9 2.7 36 11-51 69-104 (111)
56 PF01514 YscJ_FliF: Secretory 34.4 52 0.0011 24.5 3.2 21 11-31 117-137 (206)
57 PHA01634 hypothetical protein 34.2 14 0.00031 26.6 0.2 13 4-16 97-109 (156)
58 PRK11670 antiporter inner memb 34.1 2E+02 0.0042 23.3 6.7 59 11-70 67-150 (369)
59 TIGR02194 GlrX_NrdH Glutaredox 33.5 70 0.0015 19.0 3.2 41 5-58 7-47 (72)
60 PF13291 ACT_4: ACT domain; PD 33.3 49 0.0011 20.1 2.5 18 11-28 62-79 (80)
61 TIGR00401 msrA methionine-S-su 33.2 37 0.0008 24.3 2.1 28 8-35 7-34 (149)
62 TIGR00288 conserved hypothetic 33.1 69 0.0015 23.3 3.6 32 36-68 110-141 (160)
63 COG2177 FtsX Cell division pro 32.7 1.4E+02 0.003 23.7 5.5 38 8-57 71-108 (297)
64 PRK00435 ef1B elongation facto 32.1 49 0.0011 21.7 2.4 22 10-31 63-84 (88)
65 PF08478 POTRA_1: POTRA domain 31.4 84 0.0018 18.4 3.3 28 11-38 36-64 (69)
66 cd00291 SirA_YedF_YeeD SirA, Y 31.1 1.1E+02 0.0025 17.8 6.0 51 4-62 6-56 (69)
67 cd06167 LabA_like LabA_like pr 30.9 85 0.0018 21.1 3.6 29 36-65 104-132 (149)
68 PF00352 TBP: Transcription fa 30.7 71 0.0015 20.2 3.0 21 31-51 55-75 (86)
69 PF01565 FAD_binding_4: FAD bi 30.3 92 0.002 20.7 3.7 31 27-58 57-87 (139)
70 cd03422 YedF YedF is a bacteri 30.0 1.3E+02 0.0028 18.1 5.9 50 4-61 6-55 (69)
71 cd03027 GRX_DEP Glutaredoxin ( 29.8 81 0.0018 18.7 3.1 24 6-31 10-33 (73)
72 COG4004 Uncharacterized protei 29.8 52 0.0011 22.1 2.2 22 19-40 37-58 (96)
73 PF09358 UBA_e1_C: Ubiquitin-a 29.6 66 0.0014 22.2 2.9 48 34-82 35-83 (125)
74 PF07145 PAM2: Ataxin-2 C-term 29.5 29 0.00064 16.4 0.7 9 99-107 3-11 (18)
75 cd04877 ACT_TyrR N-terminal AC 29.4 60 0.0013 19.5 2.4 17 12-28 52-68 (74)
76 cd03423 SirA SirA (also known 29.4 1.3E+02 0.0029 18.0 6.2 48 4-61 6-55 (69)
77 COG0841 AcrB Cation/multidrug 29.4 1.1E+02 0.0024 28.4 5.0 46 11-57 157-211 (1009)
78 TIGR00914 2A0601 heavy metal e 29.2 76 0.0017 29.1 3.9 42 11-52 700-751 (1051)
79 PRK00058 methionine sulfoxide 29.1 46 0.001 25.4 2.2 27 8-34 52-78 (213)
80 TIGR02830 spore_III_AG stage I 29.1 51 0.0011 24.6 2.4 28 11-38 63-92 (186)
81 cd02066 GRX_family Glutaredoxi 29.0 1E+02 0.0022 17.2 3.3 17 5-22 8-24 (72)
82 PF15643 Tox-PL-2: Papain fold 28.6 63 0.0014 21.9 2.5 19 5-23 19-39 (100)
83 TIGR02189 GlrX-like_plant Glut 28.6 1.6E+02 0.0035 19.0 4.5 46 5-59 16-61 (99)
84 COG4669 EscJ Type III secretor 28.5 61 0.0013 25.3 2.8 21 10-30 110-130 (246)
85 TIGR02374 nitri_red_nirB nitri 28.3 62 0.0013 28.7 3.1 53 1-57 442-494 (785)
86 KOG4730 D-arabinono-1, 4-lacto 27.4 70 0.0015 27.5 3.1 40 19-61 99-138 (518)
87 TIGR01709 typeII_sec_gspL gene 27.2 1.8E+02 0.0039 23.3 5.4 49 13-63 314-368 (384)
88 cd03420 SirA_RHOD_Pry_redox Si 27.1 1.5E+02 0.0032 17.8 5.9 48 4-61 6-55 (69)
89 TIGR02898 spore_YhcN_YlaJ spor 27.0 1.2E+02 0.0026 22.0 3.9 30 9-38 54-83 (158)
90 COG2092 EFB1 Translation elong 26.5 60 0.0013 21.5 2.1 21 11-31 64-84 (88)
91 PRK11282 glcE glycolate oxidas 26.5 1.2E+02 0.0027 24.5 4.3 37 19-58 44-80 (352)
92 TIGR02196 GlrX_YruB Glutaredox 26.3 1.1E+02 0.0025 17.1 3.2 23 5-29 8-30 (74)
93 TIGR01617 arsC_related transcr 26.1 1.6E+02 0.0035 19.4 4.3 46 5-59 7-52 (117)
94 TIGR02544 III_secr_YscJ type I 26.0 79 0.0017 23.4 2.9 21 11-31 109-129 (193)
95 TIGR02190 GlrX-dom Glutaredoxi 26.0 97 0.0021 18.8 3.0 25 5-31 16-40 (79)
96 cd03029 GRX_hybridPRX5 Glutare 26.0 1E+02 0.0022 18.2 3.0 25 5-31 9-33 (72)
97 PF00462 Glutaredoxin: Glutare 25.3 1.4E+02 0.003 16.9 3.5 26 5-32 7-32 (60)
98 cd04909 ACT_PDH-BS C-terminal 25.2 1.5E+02 0.0032 17.1 4.7 51 8-59 12-69 (69)
99 TIGR01678 FAD_lactone_ox sugar 25.2 1.4E+02 0.0031 24.7 4.6 41 20-63 65-105 (438)
100 cd03036 ArsC_like Arsenate Red 25.0 2.1E+02 0.0045 18.8 4.6 44 5-57 7-50 (111)
101 PRK13014 methionine sulfoxide 24.8 42 0.0009 25.0 1.2 28 8-35 15-42 (186)
102 PRK10568 periplasmic protein; 24.8 1.7E+02 0.0036 21.6 4.5 35 9-43 60-96 (203)
103 COG0277 GlcD FAD/FMN-containin 24.5 87 0.0019 25.0 3.2 37 20-59 83-119 (459)
104 cd04879 ACT_3PGDH-like ACT_3PG 24.2 1E+02 0.0022 17.1 2.7 17 12-28 53-69 (71)
105 TIGR01679 bact_FAD_ox FAD-link 24.2 1.4E+02 0.0031 24.4 4.4 32 28-60 65-96 (419)
106 PF08712 Nfu_N: Scaffold prote 23.9 2.1E+02 0.0045 18.4 4.7 38 13-52 38-77 (87)
107 cd06482 ACD_HspB10 Alpha cryst 23.8 65 0.0014 20.8 1.9 23 20-42 15-39 (87)
108 PRK15348 type III secretion sy 23.8 92 0.002 24.2 3.0 21 11-31 109-129 (249)
109 PF01849 NAC: NAC domain; Int 23.7 1.2E+02 0.0027 17.8 3.0 28 12-39 2-34 (58)
110 PF13192 Thioredoxin_3: Thiore 23.7 80 0.0017 19.2 2.2 9 3-11 6-14 (76)
111 PF00873 ACR_tran: AcrB/AcrD/A 23.3 1.4E+02 0.0031 27.2 4.5 44 9-52 687-740 (1021)
112 PF04468 PSP1: PSP1 C-terminal 23.1 2.1E+02 0.0046 18.3 6.0 52 9-61 30-85 (88)
113 PF03434 DUF276: DUF276 ; Int 23.0 1.2E+02 0.0027 23.9 3.6 28 11-38 89-116 (291)
114 PF07837 FTCD_N: Formiminotran 23.0 2.4E+02 0.0053 20.9 5.0 41 11-51 18-60 (178)
115 cd00292 EF1B Elongation factor 23.0 95 0.0021 20.2 2.6 21 11-31 64-84 (88)
116 PF14847 Ras_bdg_2: Ras-bindin 23.0 62 0.0013 21.9 1.7 26 34-59 13-38 (105)
117 PRK10503 multidrug efflux syst 22.8 1.6E+02 0.0035 27.2 4.8 37 11-49 168-205 (1040)
118 PF00736 EF1_GNE: EF-1 guanine 22.7 1.2E+02 0.0025 19.8 2.9 21 11-31 64-85 (89)
119 COG0225 MsrA Peptide methionin 22.7 60 0.0013 24.1 1.7 28 8-35 13-40 (174)
120 PF07338 DUF1471: Protein of u 22.6 1E+02 0.0022 18.3 2.4 20 34-53 6-26 (56)
121 COG1782 Predicted metal-depend 22.4 2.1E+02 0.0046 25.2 5.1 60 11-70 78-143 (637)
122 PF01936 NYN: NYN domain; Int 22.4 88 0.0019 20.6 2.4 29 35-64 99-127 (146)
123 cd02977 ArsC_family Arsenate R 22.1 2.2E+02 0.0048 18.2 4.3 44 5-57 7-50 (105)
124 TIGR01677 pln_FAD_oxido plant- 21.9 1.7E+02 0.0036 25.3 4.5 33 27-60 92-124 (557)
125 PF01963 TraB: TraB family; I 21.8 2.5E+02 0.0055 20.5 5.0 27 35-62 230-259 (259)
126 cd04883 ACT_AcuB C-terminal AC 21.8 1.8E+02 0.0038 16.8 6.0 51 8-59 12-68 (72)
127 PRK10614 multidrug efflux syst 21.7 1.2E+02 0.0027 27.8 3.8 42 11-52 677-728 (1025)
128 COG3643 Glutamate formiminotra 21.6 1.1E+02 0.0023 24.4 3.0 50 11-60 20-71 (302)
129 COG3062 NapD Uncharacterized p 21.6 2.6E+02 0.0057 18.7 4.8 40 11-51 20-60 (94)
130 PF02983 Pro_Al_protease: Alph 21.6 2E+02 0.0042 17.3 4.0 19 22-40 23-41 (62)
131 cd06475 ACD_HspB1_like Alpha c 21.6 87 0.0019 19.9 2.1 22 20-41 17-40 (86)
132 TIGR02183 GRXA Glutaredoxin, G 21.6 1.3E+02 0.0028 18.8 2.9 25 6-31 9-37 (86)
133 TIGR02180 GRX_euk Glutaredoxin 21.3 1.9E+02 0.0041 17.0 4.3 46 5-57 7-52 (84)
134 cd03418 GRX_GRXb_1_3_like Glut 21.3 1.6E+02 0.0035 17.1 3.3 24 5-30 8-31 (75)
135 PF04805 Pox_E10: E10-like pro 21.2 74 0.0016 20.2 1.7 19 4-22 15-33 (70)
136 TIGR02200 GlrX_actino Glutared 20.4 1.6E+02 0.0035 16.9 3.1 19 5-25 8-26 (77)
137 PF09158 MotCF: Bacteriophage 20.2 2.9E+02 0.0062 18.8 4.5 40 20-61 39-78 (103)
138 cd06471 ACD_LpsHSP_like Group 20.1 89 0.0019 19.6 2.0 23 20-42 17-41 (93)
139 PF00873 ACR_tran: AcrB/AcrD/A 20.1 3.2E+02 0.0068 25.0 6.0 29 11-39 62-90 (1021)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.59 E-value=4.9e-15 Score=90.42 Aligned_cols=57 Identities=21% Similarity=0.404 Sum_probs=51.9
Q ss_pred Ccc-cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCC---CHHHHHHHHHHhcCCc
Q 037419 1 MRI-NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNF---IPQDLAIKIRKKTNRR 58 (110)
Q Consensus 1 lkV-gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~---d~~~I~~~I~~k~G~~ 58 (110)
|+| ||+|++|+++|+++|.+++||.++.+|+.+++++|.++. ++++|.++| +++||+
T Consensus 2 ~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i-~~~Gy~ 62 (62)
T PF00403_consen 2 FKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAI-EKAGYE 62 (62)
T ss_dssp EEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHH-HHTTSE
T ss_pred EEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHH-HHhCcC
Confidence 466 899999999999999999999999999999999998754 569999999 699984
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.47 E-value=1.7e-13 Score=87.30 Aligned_cols=62 Identities=39% Similarity=0.692 Sum_probs=56.9
Q ss_pred CcccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcC-CcEEEcc
Q 037419 1 MRINIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTN-RRVEILE 63 (110)
Q Consensus 1 lkVgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G-~~a~~~~ 63 (110)
++|+|+|.+|+.+|++.|..++||.++.+|..+++|+|.|.++|..|++.|+ +.| +++..|.
T Consensus 9 ~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~-k~~~k~~~~~~ 71 (73)
T KOG1603|consen 9 LKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLK-KTGGKRAELWK 71 (73)
T ss_pred EEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHH-hcCCCceEEec
Confidence 4789999999999999999999999999999999999999999999999995 777 7776663
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.39 E-value=1.7e-12 Score=82.37 Aligned_cols=58 Identities=17% Similarity=0.322 Sum_probs=51.7
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEE--ec-CCCHHHHHHHHHHhcCCcEEEc
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSV--SG-NFIPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV--~g-~~d~~~I~~~I~~k~G~~a~~~ 62 (110)
||+|++|+.+|+++|.+++||.++++|+..+++.| ++ .++.++|.++| +++||.+..+
T Consensus 10 ~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai-~~aGy~~~~~ 70 (71)
T COG2608 10 GMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAI-EDAGYKVEEI 70 (71)
T ss_pred CcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHH-HHcCCCeeec
Confidence 89999999999999999999999999999966665 45 47999999999 6999988654
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.14 E-value=1.2e-10 Score=88.13 Aligned_cols=65 Identities=17% Similarity=0.308 Sum_probs=61.1
Q ss_pred cccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEcccccC
Q 037419 2 RINIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEILEIHEF 67 (110)
Q Consensus 2 kVgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~~~~p~ 67 (110)
.|.|+|++|++.|+..|..++||.+|++|+.++.|.|.+...+++|...| +.+|++|.+.+.+..
T Consensus 12 aV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~l-e~tGr~Avl~G~G~p 76 (247)
T KOG4656|consen 12 AVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTL-ENTGRDAVLRGAGKP 76 (247)
T ss_pred EEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHH-HhhChheEEecCCch
Confidence 58999999999999999999999999999999999999999999999999 699999999876543
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.72 E-value=7e-08 Score=73.63 Aligned_cols=67 Identities=15% Similarity=0.345 Sum_probs=60.2
Q ss_pred CcccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEcccccCC
Q 037419 1 MRINIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEILEIHEFS 68 (110)
Q Consensus 1 lkVgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~~~~p~~ 68 (110)
+.|+|+|++|+.+|+++|.+++||.++.+++..++++|.+..++..+...+ +++||.+++++..+.+
T Consensus 10 ~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aI-e~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 10 FMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAAL-EQTGRKARLIGQGDPE 76 (238)
T ss_pred EEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHH-HHcCCcEEEecCCCcc
Confidence 357899999999999999999999999999999999998777889999999 6999999888775554
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.44 E-value=5.5e-07 Score=78.76 Aligned_cols=57 Identities=18% Similarity=0.366 Sum_probs=51.0
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEcc
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEILE 63 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~~ 63 (110)
||+|++|+.+|+++|.+++||..+.+|+. +.+|.+..+++.+.+.+ +++||+++...
T Consensus 11 gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i-~~~Gy~~~~~~ 67 (834)
T PRK10671 11 GLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETI-KQAGYDASVSH 67 (834)
T ss_pred CcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHH-HhcCCcccccc
Confidence 89999999999999999999999999995 45566667999999999 69999998764
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.15 E-value=4.8e-06 Score=72.44 Aligned_cols=56 Identities=18% Similarity=0.376 Sum_probs=50.8
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecC---CC-HHHHHHHHHHhcCCcEEE
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGN---FI-PQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~---~d-~~~I~~~I~~k~G~~a~~ 61 (110)
||+|..|+.+|| +|.+++||.++.+|+.++++.|..+ .+ ++.+...+ ++.||.+..
T Consensus 10 Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v-~~~gy~~~~ 69 (713)
T COG2217 10 GMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAV-EKAGYSARL 69 (713)
T ss_pred CcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHH-HhcCccccc
Confidence 899999999999 9999999999999999999999743 35 78999999 699998876
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.74 E-value=0.00032 Score=38.99 Aligned_cols=55 Identities=15% Similarity=0.230 Sum_probs=45.8
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEec---CCCHHHHHHHHHHhcCCcE
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSG---NFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g---~~d~~~I~~~I~~k~G~~a 59 (110)
+|+|..|+..+++.+...+++....+++..+.+.+.. ..+...+...+ ...|+.+
T Consensus 10 ~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~g~~~ 67 (68)
T TIGR00003 10 SMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAI-LDAGYEV 67 (68)
T ss_pred CeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHH-HHcCCCc
Confidence 7899999999999999999999999999999988863 24677777777 5778743
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.63 E-value=0.00012 Score=65.18 Aligned_cols=67 Identities=15% Similarity=0.262 Sum_probs=59.1
Q ss_pred ccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEec--CCCHHHHHHHHHHhcCCcEEEcccccCCCC
Q 037419 3 INIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSG--NFIPQDLAIKIRKKTNRRVEILEIHEFSSN 70 (110)
Q Consensus 3 VgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g--~~d~~~I~~~I~~k~G~~a~~~~~~p~~~~ 70 (110)
.||+|..|.+.|++++.+.+||.++.+++.+++.+|.. ..+++.+.+.| +..|+++.+.........
T Consensus 1 ~gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~i-ed~gf~~~~~~~~~~~~~ 69 (951)
T KOG0207|consen 1 KGMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETI-EDMGFEASLLSDSEITAS 69 (951)
T ss_pred CCccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHh-hcccceeeecccCccccc
Confidence 48999999999999999999999999999998888864 35899999999 799999998876665554
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.51 E-value=0.00024 Score=63.22 Aligned_cols=82 Identities=18% Similarity=0.284 Sum_probs=62.8
Q ss_pred ccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecC---CCHHHHHHHHHHhcCCcEEEcccccCCCCCCCcchhhh
Q 037419 3 INIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGN---FIPQDLAIKIRKKTNRRVEILEIHEFSSNNNNIIEGHQ 79 (110)
Q Consensus 3 VgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~---~d~~~I~~~I~~k~G~~a~~~~~~p~~~~~~~~~~~h~ 79 (110)
.||+|.+|..+|++.|.+++||.++++++.++++.|... ..|-.+++.| +.+|+.+...........+ +=.|+
T Consensus 153 ~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~i-e~~~~~~~~~~~~~~~~~~---~l~~~ 228 (951)
T KOG0207|consen 153 LGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAI-EETGFEASVRPYGDTTFKN---SLKHK 228 (951)
T ss_pred ecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHH-Hhhcccceeeeccccchhh---hhhhh
Confidence 389999999999999999999999999999999998642 4789999999 6999988776654433332 22344
Q ss_pred HHhhhcCCc
Q 037419 80 EQLLQDQRP 88 (110)
Q Consensus 80 ~~~~~~~~~ 88 (110)
++..++.++
T Consensus 229 ~ei~~w~~~ 237 (951)
T KOG0207|consen 229 EEIRKWKRP 237 (951)
T ss_pred hHHHhcchH
Confidence 544444433
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.51 E-value=0.00027 Score=62.07 Aligned_cols=58 Identities=22% Similarity=0.384 Sum_probs=52.1
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEc
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~ 62 (110)
||+|.+|+.+|++.+.+++||.++.+++.++++.+.+..++..+.+.+ ++.||.+.++
T Consensus 107 Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I-~~~Gy~a~~~ 164 (834)
T PRK10671 107 GMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAV-EKAGYGAEAI 164 (834)
T ss_pred CcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHH-HhcCCCcccc
Confidence 899999999999999999999999999999998887666888888889 5999987654
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.09 E-value=0.0013 Score=57.40 Aligned_cols=58 Identities=17% Similarity=0.279 Sum_probs=48.0
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCC-CHHHHHHHHHHhcCCcEEEc
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNF-IPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~-d~~~I~~~I~~k~G~~a~~~ 62 (110)
||+|.+|+.+|++.+.+++||.++.+++.++++.+.... ....+...+ +++||.+...
T Consensus 61 Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI-~~~Gy~a~~~ 119 (741)
T PRK11033 61 GMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAV-QKAGFSLRDE 119 (741)
T ss_pred CCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHH-Hhcccccccc
Confidence 799999999999999999999999999999998886321 226677788 5899977543
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=94.40 E-value=0.56 Score=28.34 Aligned_cols=57 Identities=14% Similarity=0.156 Sum_probs=43.4
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEe--c-CCCHHHHHHHHHHhcCCcEEE
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVS--G-NFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~--g-~~d~~~I~~~I~~k~G~~a~~ 61 (110)
++.|..|...++..+...+|+....++.....+.+. + ..+...+...+ ...|+.+++
T Consensus 31 ~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~g~~~~~ 90 (92)
T TIGR02052 31 GMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEAT-TDAGYPSSL 90 (92)
T ss_pred CeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHH-HhcCCCeEe
Confidence 678999999999999999998888888888776664 2 23566666666 477876543
No 14
>PRK13748 putative mercuric reductase; Provisional
Probab=93.28 E-value=0.63 Score=38.78 Aligned_cols=60 Identities=15% Similarity=0.271 Sum_probs=48.2
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEec--CCCHHHHHHHHHHhcCCcEEEccc
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSG--NFIPQDLAIKIRKKTNRRVEILEI 64 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g--~~d~~~I~~~I~~k~G~~a~~~~~ 64 (110)
+|+|.+|..+++..+..++++....+++..+.+.+.. ..+...+...+ ...|+..++...
T Consensus 8 g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i-~~~g~~~~~~~~ 69 (561)
T PRK13748 8 GMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAV-AGLGYRATLADA 69 (561)
T ss_pred CeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHH-HHcCCeeeccCc
Confidence 7899999999999999999999899999888877752 24566676777 588987665555
No 15
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=89.18 E-value=1.6 Score=21.26 Aligned_cols=48 Identities=25% Similarity=0.497 Sum_probs=34.2
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecC--CCHHHHHHHH
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGN--FIPQDLAIKI 51 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~--~d~~~I~~~I 51 (110)
++.|..|...++..+...+|+.....++....+.+... .+...+...+
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAI 55 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHH
Confidence 68899999999999999999877777776666555422 2444444444
No 16
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=83.26 E-value=5.2 Score=26.90 Aligned_cols=48 Identities=10% Similarity=0.202 Sum_probs=33.8
Q ss_pred HHHHHhcCCCeeEEEEe-----c--cCCEEEEecC-CCHHHHHHHHHHhcCCcEEEc
Q 037419 14 VRRALLDMQELESHLIE-----K--KMCRVSVSGN-FIPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 14 IekaL~~l~GV~~v~vd-----~--~~~kVtV~g~-~d~~~I~~~I~~k~G~~a~~~ 62 (110)
+-+.|.+++||+.|.+. . .+=+++|.|+ .|-++|.+.| ++.|-.++.+
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~i-E~~Gg~IHSi 79 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVI-EELGGAIHSI 79 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHH-HHcCCeeeeh
Confidence 34567788887755433 3 3456667774 6999999999 6999866554
No 17
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=82.72 E-value=7.1 Score=26.29 Aligned_cols=50 Identities=10% Similarity=0.274 Sum_probs=34.4
Q ss_pred HHHHHHhcCCCeeEEEEec-----cCC--EEEEecC-CCHHHHHHHHHHhcCCcEEEcc
Q 037419 13 KVRRALLDMQELESHLIEK-----KMC--RVSVSGN-FIPQDLAIKIRKKTNRRVEILE 63 (110)
Q Consensus 13 kIekaL~~l~GV~~v~vd~-----~~~--kVtV~g~-~d~~~I~~~I~~k~G~~a~~~~ 63 (110)
.+-++|.+++||..|.+.+ .+. +++|+|. +|.++|.++| ++.|-.++.+.
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~I-e~~Gg~IHSID 78 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAI-EELGGVIHSID 78 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHH-HHTT-EEEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHH-HHcCCeEEeee
Confidence 3557889999998766544 333 4455675 6999999999 69998766543
No 18
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=78.48 E-value=7.4 Score=23.48 Aligned_cols=52 Identities=15% Similarity=0.121 Sum_probs=34.7
Q ss_pred ccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEc
Q 037419 3 INIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 3 VgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~ 62 (110)
.|+.|+...-+++++|.+++.=+.+.+ .++.......|...+ ++.|++...+
T Consensus 6 rg~~CP~Pll~~~~~l~~l~~G~~l~v-------~~d~~~~~~di~~~~-~~~g~~~~~~ 57 (70)
T PF01206_consen 6 RGLSCPMPLLKAKKALKELPPGEVLEV-------LVDDPAAVEDIPRWC-EENGYEVVEV 57 (70)
T ss_dssp SS-STTHHHHHHHHHHHTSGTT-EEEE-------EESSTTHHHHHHHHH-HHHTEEEEEE
T ss_pred CCCCCCHHHHHHHHHHHhcCCCCEEEE-------EECCccHHHHHHHHH-HHCCCEEEEE
Confidence 378999999999999999853222221 112334567888888 6999975443
No 19
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=75.92 E-value=2.5 Score=25.82 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=15.1
Q ss_pred HHHHHHHHhcCCCeeEEEE
Q 037419 11 YRKVRRALLDMQELESHLI 29 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~v 29 (110)
...|+++|..++||.+|.|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 3788999999999998875
No 20
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=75.58 E-value=9.1 Score=27.61 Aligned_cols=60 Identities=7% Similarity=0.092 Sum_probs=43.0
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEecC----C--CHHHHHHHHHHhcCCcEEEcccccCCCC
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVSGN----F--IPQDLAIKIRKKTNRRVEILEIHEFSSN 70 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~g~----~--d~~~I~~~I~~k~G~~a~~~~~~p~~~~ 70 (110)
...|++.+-.-.||.++.+|..+|.|.|... + -....+..|..++|+...++...|..+.
T Consensus 55 ~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpPi~S~ 120 (145)
T cd02410 55 IKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPPIQSR 120 (145)
T ss_pred HHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCCCCcH
Confidence 4456666655568999999999999999621 1 2234444555799999999888887666
No 21
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=67.44 E-value=26 Score=21.50 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=31.2
Q ss_pred HHhcCCCeeEEEEeccCC--EEEEecCCCHHHHHHHHHHhcCCcEEEcc
Q 037419 17 ALLDMQELESHLIEKKMC--RVSVSGNFIPQDLAIKIRKKTNRRVEILE 63 (110)
Q Consensus 17 aL~~l~GV~~v~vd~~~~--kVtV~g~~d~~~I~~~I~~k~G~~a~~~~ 63 (110)
.|..++||.++..+ ..+ ++.+....+..+|++.+ ...|. +.-..
T Consensus 25 ~l~~~~~v~~v~~~-~~~~~~i~l~~~~~~~~ll~~l-~~~g~-I~~f~ 70 (84)
T PF13732_consen 25 ELEELPGVESVEQD-GDGKLRIKLEDEETANELLQEL-IEKGI-IRSFE 70 (84)
T ss_pred HHhhCCCeEEEEEe-CCcEEEEEECCcccHHHHHHHH-HhCCC-eeEEE
Confidence 37888999988764 344 44445556889999999 58888 55433
No 22
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=65.78 E-value=34 Score=25.10 Aligned_cols=64 Identities=17% Similarity=0.315 Sum_probs=40.2
Q ss_pred CcccccchhHHHHHH------------HHHhcC------CCeeEEEEeccCCEEEE-e--cC---C-CHHHHHHHHHHhc
Q 037419 1 MRINIDCNGCYRKVR------------RALLDM------QELESHLIEKKMCRVSV-S--GN---F-IPQDLAIKIRKKT 55 (110)
Q Consensus 1 lkVgM~C~~Ca~kIe------------kaL~~l------~GV~~v~vd~~~~kVtV-~--g~---~-d~~~I~~~I~~k~ 55 (110)
+|-|+-|+.|.++++ ++|.+| .++.-.+.-...+++.+ . |. + .--..+++++++.
T Consensus 10 ~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l~~~l 89 (166)
T PRK06418 10 VKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKALSRKL 89 (166)
T ss_pred eccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHHHHHh
Confidence 366888999999864 566665 34443332223455553 2 32 1 2245677787899
Q ss_pred CCcEEEccc
Q 037419 56 NRRVEILEI 64 (110)
Q Consensus 56 G~~a~~~~~ 64 (110)
|++++++.+
T Consensus 90 gk~VevVE~ 98 (166)
T PRK06418 90 GKKVRVVEK 98 (166)
T ss_pred CCcEEEEEc
Confidence 999999875
No 23
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=65.47 E-value=30 Score=22.64 Aligned_cols=29 Identities=10% Similarity=0.070 Sum_probs=23.3
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS 39 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~ 39 (110)
...+.++|..+||++=...|...||+.|+
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVt 47 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVV 47 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEE
Confidence 56789999999999855566777888875
No 24
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=60.66 E-value=6.2 Score=24.30 Aligned_cols=20 Identities=25% Similarity=0.657 Sum_probs=17.2
Q ss_pred CcccccchhHHHHHHHHHhc
Q 037419 1 MRINIDCNGCYRKVRRALLD 20 (110)
Q Consensus 1 lkVgM~C~~Ca~kIekaL~~ 20 (110)
++++-.|++|...|++.|.+
T Consensus 33 ~~~g~~CG~C~~~i~~il~~ 52 (64)
T PRK10509 33 VPVGNQCGKCIRAAREVMQD 52 (64)
T ss_pred cCCCCCccchHHHHHHHHHH
Confidence 46889999999999998864
No 25
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=58.10 E-value=38 Score=20.19 Aligned_cols=49 Identities=12% Similarity=0.202 Sum_probs=33.2
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEE
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
|+.|+.-.-+.+++| ++..=+.+.+- ++.......|...+ ++.|+....
T Consensus 6 G~~CP~P~l~~k~al-~~~~g~~l~v~-------~d~~~s~~~i~~~~-~~~G~~~~~ 54 (67)
T cd03421 6 GLACPQPVIKTKKAL-ELEAGGEIEVL-------VDNEVAKENVSRFA-ESRGYEVSV 54 (67)
T ss_pred CCCCCHHHHHHHHHH-hcCCCCEEEEE-------EcChhHHHHHHHHH-HHcCCEEEE
Confidence 789999999999999 66432222221 22233457888888 699998743
No 26
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=55.36 E-value=8.6 Score=22.59 Aligned_cols=31 Identities=26% Similarity=0.267 Sum_probs=16.8
Q ss_pred HHHHHHHhc---CCCeeEEEEeccCCEEEEecCCC
Q 037419 12 RKVRRALLD---MQELESHLIEKKMCRVSVSGNFI 43 (110)
Q Consensus 12 ~kIekaL~~---l~GV~~v~vd~~~~kVtV~g~~d 43 (110)
.+|+++|.. +++- .+.+....+.|++.|.++
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~ 35 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEVP 35 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEES
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeCc
Confidence 467777776 4444 678888999999999763
No 27
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=54.13 E-value=17 Score=21.60 Aligned_cols=20 Identities=10% Similarity=0.129 Sum_probs=16.7
Q ss_pred HHHHHHHHHhcCCCeeEEEE
Q 037419 10 CYRKVRRALLDMQELESHLI 29 (110)
Q Consensus 10 Ca~kIekaL~~l~GV~~v~v 29 (110)
--..|.+.|++++||.+|.+
T Consensus 55 ~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 55 DIDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHHhcCCCeEEEEE
Confidence 45778899999999998864
No 28
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=52.99 E-value=75 Score=22.09 Aligned_cols=50 Identities=22% Similarity=0.258 Sum_probs=33.9
Q ss_pred HHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHH----HHhcCCcEEEc
Q 037419 12 RKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKI----RKKTNRRVEIL 62 (110)
Q Consensus 12 ~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I----~~k~G~~a~~~ 62 (110)
..++..|.++ |-..|..=..+|-|.+....++..+...| .+..|+.+.++
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 5677888887 78899999999999999767776665554 45788876543
No 29
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=52.58 E-value=36 Score=24.97 Aligned_cols=28 Identities=11% Similarity=0.202 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCCE
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMCR 35 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~k 35 (110)
+||-.-++..+.+++||.++.+=+..+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 5788899999999999999998887765
No 30
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=51.90 E-value=25 Score=25.38 Aligned_cols=32 Identities=19% Similarity=0.217 Sum_probs=26.4
Q ss_pred cchhHHHHHHHHHhcCCCeeEEEEecc-CCEEEE
Q 037419 6 DCNGCYRKVRRALLDMQELESHLIEKK-MCRVSV 38 (110)
Q Consensus 6 ~C~~Ca~kIekaL~~l~GV~~v~vd~~-~~kVtV 38 (110)
.|..|..-|.+...++ |+.++.|... ++++.+
T Consensus 110 vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 110 VCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVYY 142 (146)
T ss_pred cchHHHHHHHHHHHHc-CCCeEEEEecCCCcEEE
Confidence 4999999999988886 7999988877 776654
No 31
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=49.71 E-value=19 Score=23.27 Aligned_cols=21 Identities=19% Similarity=0.151 Sum_probs=17.8
Q ss_pred HHHHHHHhcCCCeeEEEEecc
Q 037419 12 RKVRRALLDMQELESHLIEKK 32 (110)
Q Consensus 12 ~kIekaL~~l~GV~~v~vd~~ 32 (110)
..|+.+|..++|+.++.+++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 458889999999999988874
No 32
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=48.44 E-value=14 Score=27.17 Aligned_cols=20 Identities=15% Similarity=0.273 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCeeEEEEec
Q 037419 12 RKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 12 ~kIekaL~~l~GV~~v~vd~ 31 (110)
..|+.+|..++||.++.|++
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHhCCCceeEEEEE
Confidence 45889999999999888876
No 33
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=48.42 E-value=35 Score=24.16 Aligned_cols=28 Identities=7% Similarity=0.030 Sum_probs=25.2
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEE
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSV 38 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV 38 (110)
+.+|.+.+.+++||.++.+=.....+.|
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~V 104 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYV 104 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEE
Confidence 6789999999999999999888888877
No 34
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=47.73 E-value=70 Score=20.21 Aligned_cols=40 Identities=18% Similarity=0.243 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe-cCCCHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS-GNFIPQDLAIKI 51 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~-g~~d~~~I~~~I 51 (110)
...+.++|..+||++=...+.. +|+.|+ -..+...+.+.+
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~ 57 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLI 57 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHH
Confidence 4678999999999975556555 777775 233555555555
No 35
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=46.62 E-value=40 Score=30.92 Aligned_cols=42 Identities=7% Similarity=0.017 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe--------cCCCHHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS--------GNFIPQDLAIKIR 52 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~--------g~~d~~~I~~~I~ 52 (110)
+..++..|.+++||.+|++.-....+.|. -.+++.+|.++|+
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~ 208 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIE 208 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 46799999999999999988665656664 2468899999994
No 36
>PRK09577 multidrug efflux protein; Reviewed
Probab=45.46 E-value=65 Score=29.61 Aligned_cols=46 Identities=15% Similarity=0.104 Sum_probs=35.8
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe--------cCCCHHHHHHHHHHhcCC
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS--------GNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~--------g~~d~~~I~~~I~~k~G~ 57 (110)
+..|+..|.++|||.+|+++-....+.|. -.+++.+|.++|+ ..+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~-~~n~ 211 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVR-AHNA 211 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHH-HhCC
Confidence 46799999999999999998766666663 2468899999994 5443
No 37
>PRK11018 hypothetical protein; Provisional
Probab=45.20 E-value=75 Score=19.84 Aligned_cols=51 Identities=10% Similarity=-0.010 Sum_probs=35.2
Q ss_pred ccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEE
Q 037419 3 INIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 3 VgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
.|+.|+.-.-+.+++|.+++.-+.+.|- ++.......|...+ ++.|+++..
T Consensus 14 rG~~CP~Pvl~~kk~l~~l~~G~~L~V~-------~d~~~a~~di~~~~-~~~G~~v~~ 64 (78)
T PRK11018 14 VGEPCPYPAVATLEALPQLKKGEILEVV-------SDCPQSINNIPLDA-RNHGYTVLD 64 (78)
T ss_pred CCCcCCHHHHHHHHHHHhCCCCCEEEEE-------eCCccHHHHHHHHH-HHcCCEEEE
Confidence 3789999999999999998632222221 12334567788888 699997743
No 38
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=43.24 E-value=60 Score=20.09 Aligned_cols=50 Identities=16% Similarity=0.174 Sum_probs=33.8
Q ss_pred HHHHHHHHhcC---CCeeEEEEeccCCEEEEe--cCCCHHHHHHHHHHhcCCcEE
Q 037419 11 YRKVRRALLDM---QELESHLIEKKMCRVSVS--GNFIPQDLAIKIRKKTNRRVE 60 (110)
Q Consensus 11 a~kIekaL~~l---~GV~~v~vd~~~~kVtV~--g~~d~~~I~~~I~~k~G~~a~ 60 (110)
..++.++|.++ +.--.+..|-.++.+.|. |.+-.+-++++|+++.|..++
T Consensus 18 ~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 18 EPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp HHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred HHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 34566666554 223368889999999987 456778888899656665554
No 39
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=43.05 E-value=21 Score=25.85 Aligned_cols=28 Identities=14% Similarity=0.198 Sum_probs=23.8
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCCE
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMCR 35 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~k 35 (110)
+||=.-++..+.+++||.++.+=+..+.
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 35 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGR 35 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCC
Confidence 5788889999999999999998776644
No 40
>PRK11023 outer membrane lipoprotein; Provisional
Probab=42.61 E-value=63 Score=23.69 Aligned_cols=41 Identities=15% Similarity=0.150 Sum_probs=30.3
Q ss_pred HHHHHHHHhcCCCee---EEEEeccCCEEEEecCCCHHHHHHHH
Q 037419 11 YRKVRRALLDMQELE---SHLIEKKMCRVSVSGNFIPQDLAIKI 51 (110)
Q Consensus 11 a~kIekaL~~l~GV~---~v~vd~~~~kVtV~g~~d~~~I~~~I 51 (110)
+.+|+.+|..-+++. .+.|....|.|++.|.++.+......
T Consensus 51 ~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A 94 (191)
T PRK11023 51 ELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERA 94 (191)
T ss_pred HHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHH
Confidence 567888888767663 58888899999999988554444333
No 41
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=42.15 E-value=28 Score=22.86 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=18.1
Q ss_pred HHHHHHHHhcCCCeeEEEEec
Q 037419 11 YRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~ 31 (110)
...|+.++++++||+++++-.
T Consensus 64 td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 64 TEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred hHHHHHHHhcCCCccEEEEEE
Confidence 478999999999999998753
No 42
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=41.90 E-value=71 Score=27.95 Aligned_cols=61 Identities=8% Similarity=0.113 Sum_probs=43.7
Q ss_pred HHHHHHHHHhcCCCeeEEEEeccCCEEEEecC----C--CHHHHHHHHHHhcCCcEEEcccccCCCC
Q 037419 10 CYRKVRRALLDMQELESHLIEKKMCRVSVSGN----F--IPQDLAIKIRKKTNRRVEILEIHEFSSN 70 (110)
Q Consensus 10 Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~----~--d~~~I~~~I~~k~G~~a~~~~~~p~~~~ 70 (110)
-...|++.+-+-.||.++.+|..++.|.|+.. + .....++.|.+++|++..++...|..+.
T Consensus 71 ~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~~~~~ 137 (630)
T TIGR03675 71 AIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPPIESK 137 (630)
T ss_pred HHHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCCCCcH
Confidence 34567777766679999999999999999621 1 1223334444799999999888787666
No 43
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=41.78 E-value=1.1e+02 Score=22.59 Aligned_cols=51 Identities=14% Similarity=0.136 Sum_probs=35.7
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEc
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~ 62 (110)
|+.|+.-.-+.+++|.+++.-+.+.| .++.......|.+.+ +..||++...
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~g~~L~V-------lvD~~~a~~nV~~~~-~~~G~~v~~~ 55 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGEEGVLTV-------IVDNEAAKENVSKFA-TSLGYEVEVE 55 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCEEEE-------EECCccHHHHHHHHH-HHcCCEEEEE
Confidence 78999999999999999862111211 222334567888888 6999988643
No 44
>PRK11023 outer membrane lipoprotein; Provisional
Probab=40.95 E-value=94 Score=22.75 Aligned_cols=40 Identities=18% Similarity=0.175 Sum_probs=26.4
Q ss_pred HHHHHHHHHhcCCCee--EEEEeccCCEEEEecCCCHHHHHH
Q 037419 10 CYRKVRRALLDMQELE--SHLIEKKMCRVSVSGNFIPQDLAI 49 (110)
Q Consensus 10 Ca~kIekaL~~l~GV~--~v~vd~~~~kVtV~g~~d~~~I~~ 49 (110)
=..+|+.+|..-+++. .+.|...+|.|++.|.++..+...
T Consensus 128 It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~~ 169 (191)
T PRK11023 128 ITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAKA 169 (191)
T ss_pred HHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHHH
Confidence 4567888887766655 445555678888888776655433
No 45
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=40.81 E-value=58 Score=30.03 Aligned_cols=42 Identities=7% Similarity=0.070 Sum_probs=33.2
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe--------cCCCHHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS--------GNFIPQDLAIKIR 52 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~--------g~~d~~~I~~~I~ 52 (110)
++.|+..|.+++||.++++.-....+.|. -.+++.+|.++|+
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~ 208 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIK 208 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHH
Confidence 35799999999999999987665557764 2468888899994
No 46
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=40.23 E-value=45 Score=20.54 Aligned_cols=27 Identities=7% Similarity=0.358 Sum_probs=18.9
Q ss_pred ccchhHHHHHHHHHhcC----CCeeEEEEecc
Q 037419 5 IDCNGCYRKVRRALLDM----QELESHLIEKK 32 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l----~GV~~v~vd~~ 32 (110)
-.|+.| .++++.|.++ .||.-..+|..
T Consensus 9 ~~C~~C-~~a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 9 PGCPYC-VRAKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred CCChhH-HHHHHHHHhhcccccCCcEEEEECC
Confidence 369999 6778888876 56665555554
No 47
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=38.97 E-value=37 Score=20.33 Aligned_cols=38 Identities=11% Similarity=0.088 Sum_probs=23.9
Q ss_pred HHHHHhcCCCeeEEEEecc----CC-EEE--EecCCCHHHHHHHHHH
Q 037419 14 VRRALLDMQELESHLIEKK----MC-RVS--VSGNFIPQDLAIKIRK 53 (110)
Q Consensus 14 IekaL~~l~GV~~v~vd~~----~~-kVt--V~g~~d~~~I~~~I~~ 53 (110)
||.+|.+++||.++.|=.. .+ .+. |.. +.++|.+.++.
T Consensus 2 IE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~--~~~~i~~~~~~ 46 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVL--DEEEIRDHLRD 46 (73)
T ss_dssp HHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEE--HHHHHHHHHHH
T ss_pred HHHHHhcCCCccEEEEEEEEcccccccceeEEEe--eecccccchhh
Confidence 8999999999987764331 12 222 123 55777777753
No 48
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=38.76 E-value=94 Score=23.45 Aligned_cols=29 Identities=17% Similarity=0.291 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCeeEEEEeccCCEEEEecC
Q 037419 12 RKVRRALLDMQELESHLIEKKMCRVSVSGN 41 (110)
Q Consensus 12 ~kIekaL~~l~GV~~v~vd~~~~kVtV~g~ 41 (110)
..+.+.|....|+. +.+|..++.|+|...
T Consensus 27 g~v~k~ie~~~~~~-~~iD~~~~~V~i~~~ 55 (194)
T COG1094 27 GEVKKAIEEKTGVK-LRIDSKTGSVTIRTT 55 (194)
T ss_pred ccchHHHHhhcCeE-EEEECCCCeEEEEec
Confidence 35677888877774 889999999999643
No 49
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=38.58 E-value=62 Score=29.79 Aligned_cols=42 Identities=7% Similarity=0.093 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe--------cCCCHHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS--------GNFIPQDLAIKIR 52 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~--------g~~d~~~I~~~I~ 52 (110)
+..|+..|.+++||.+|++.-....+.|. -.+++.+|.++|+
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~ 208 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQ 208 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 35799999999999999998776667775 2468899999995
No 50
>PF08210 APOBEC_N: APOBEC-like N-terminal domain; InterPro: IPR013158 This domain is found at the N terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination. APOBEC-3 like members contain two copies of this domain. This family also includes the functionally homologous activation induced deaminase, which is essential for the development of antibody diversity in B lymphocytes. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome [] (and references therein).; GO: 0008270 zinc ion binding, 0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; PDB: 3IQS_A 3IR2_A 3V4J_B 2KEM_A 2KBO_A 3V4K_A 3E1U_A 2JYW_A 2RPZ_A.
Probab=38.47 E-value=49 Score=24.37 Aligned_cols=56 Identities=18% Similarity=0.210 Sum_probs=35.2
Q ss_pred chh----HHHHHHHHHhcC--CCeeEEEEeccCCEEEEecCCC---HHHHHHHHHHhcCCcEEEccccc
Q 037419 7 CNG----CYRKVRRALLDM--QELESHLIEKKMCRVSVSGNFI---PQDLAIKIRKKTNRRVEILEIHE 66 (110)
Q Consensus 7 C~~----Ca~kIekaL~~l--~GV~~v~vd~~~~kVtV~g~~d---~~~I~~~I~~k~G~~a~~~~~~p 66 (110)
|.. |+.+|-..|.+. ++|. +.+-.+ ++--...-. -.+=+..+ .++|-++++++..+
T Consensus 85 C~~~~~~Ca~~i~~FL~~~~~~~v~-L~I~~a--rLY~~~~~~~~~~~eGLr~L-~~aGv~v~iM~~~d 149 (188)
T PF08210_consen 85 CPESDHCCAEKIAEFLKKHLKPNVS-LSIFAA--RLYYHWEPEPLWNQEGLRRL-ASAGVQVEIMSYKD 149 (188)
T ss_dssp -CC----HHHHHHHHHCCC--TTEE-EEEEES--S--STTSTT---HHHHHHHH-HHCTEEEEE-SHHH
T ss_pred CcchhhHHHHHHHHHHHHhCCCCCe-EEEEEE--eeeeecCCcchhHHHHHHHH-HHcCCEEEEcCHHH
Confidence 888 999999999999 8884 444322 222111222 35666677 48899999886654
No 51
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=37.48 E-value=38 Score=24.34 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCC
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMC 34 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~ 34 (110)
.||-..++..+.+++||.++.+=+..+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG 33 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGG 33 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence 478888999999999999999988766
No 52
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=35.86 E-value=69 Score=27.66 Aligned_cols=39 Identities=23% Similarity=0.216 Sum_probs=31.7
Q ss_pred HhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcE
Q 037419 18 LLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 18 L~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a 59 (110)
|.++.+| +++|..+++|+|.+.+...+|...+ .+.|+..
T Consensus 110 L~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L-~~~Glal 148 (541)
T TIGR01676 110 LALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAI-KEYGITL 148 (541)
T ss_pred hhhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHH-HHcCCEe
Confidence 3455665 4678889999999999999999999 5999855
No 53
>PF04324 Fer2_BFD: BFD-like [2Fe-2S] binding domain; InterPro: IPR007419 The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as bacterioferritin-associated ferredoxin (BFD, P13655 from SWISSPROT). The function of BFD is not known, but it may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria []. This domain is also found in nitrate reductase proteins in association with the nitrite and sulphite reductase 4Fe-4S domain (IPR006067 from INTERPRO), nitrite/sulphite reductase ferredoxin-like half domain (IPR005117 from INTERPRO) and pyridine nucleotide-disulphide oxidoreductase (IPR001327 from INTERPRO). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N-terminal domain (IPR002871 from INTERPRO) and C-terminal domain (IPR001075 from INTERPRO).; PDB: 2HU9_A.
Probab=35.73 E-value=11 Score=21.84 Aligned_cols=19 Identities=21% Similarity=0.548 Sum_probs=4.7
Q ss_pred cccccchhHHHHHHHHHhc
Q 037419 2 RINIDCNGCYRKVRRALLD 20 (110)
Q Consensus 2 kVgM~C~~Ca~kIekaL~~ 20 (110)
++|..|++|...|++.|..
T Consensus 35 ~~g~~Cg~C~~~v~~ll~e 53 (55)
T PF04324_consen 35 GAGTGCGSCVPEVKDLLAE 53 (55)
T ss_dssp TTSS-TH------------
T ss_pred CCCCCCCCccccccccccc
Confidence 4688899999988877753
No 54
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=35.67 E-value=95 Score=21.77 Aligned_cols=47 Identities=13% Similarity=0.078 Sum_probs=29.3
Q ss_pred HHHHHHHHhcCC-CeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCC
Q 037419 11 YRKVRRALLDMQ-ELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 11 a~kIekaL~~l~-GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~ 57 (110)
+..|+++|.+.. +...+.|....+.|++.|.+.......++...+|.
T Consensus 28 ~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~~aa~~ 75 (147)
T PRK11198 28 ADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKILLAVGN 75 (147)
T ss_pred HHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHHHHhcc
Confidence 466777776531 24456777789999999987544444444234443
No 55
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=35.05 E-value=44 Score=22.88 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKI 51 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I 51 (110)
...++++|..++||.++.|++. ....-.++.+....
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l~-----~~p~Wt~~~ms~ea 104 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVELT-----LSPPWTPDRMSEEA 104 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEEE-----EcCCCchhhcCHHH
Confidence 5789999999999999988762 22223455555544
No 56
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=34.40 E-value=52 Score=24.49 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=18.2
Q ss_pred HHHHHHHHhcCCCeeEEEEec
Q 037419 11 YRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~ 31 (110)
...+++.|..++||.+++|.+
T Consensus 117 e~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEEE
Confidence 467899999999999998875
No 57
>PHA01634 hypothetical protein
Probab=34.19 E-value=14 Score=26.65 Aligned_cols=13 Identities=38% Similarity=0.935 Sum_probs=10.6
Q ss_pred cccchhHHHHHHH
Q 037419 4 NIDCNGCYRKVRR 16 (110)
Q Consensus 4 gM~C~~Ca~kIek 16 (110)
-|+|+||+++|.-
T Consensus 97 ~iDCeGCE~~l~v 109 (156)
T PHA01634 97 VMDCEGCEEKLNV 109 (156)
T ss_pred EEEccchHHhcCH
Confidence 4899999988753
No 58
>PRK11670 antiporter inner membrane protein; Provisional
Probab=34.10 E-value=2e+02 Score=23.29 Aligned_cols=59 Identities=17% Similarity=0.243 Sum_probs=40.0
Q ss_pred HHHHHHHHhcCCCeeEEEEeccC------------------CEEEEe---cCC----CHHHHHHHHHHhcCCcEEEcccc
Q 037419 11 YRKVRRALLDMQELESHLIEKKM------------------CRVSVS---GNF----IPQDLAIKIRKKTNRRVEILEIH 65 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~------------------~kVtV~---g~~----d~~~I~~~I~~k~G~~a~~~~~~ 65 (110)
...++.+|..++||.++.+.+.. +.+.|. |.+ -...|...+ .+.|+++-++.-.
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA~aL-A~~G~rVlLID~D 145 (369)
T PRK11670 67 KEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALAL-AAEGAKVGILDAD 145 (369)
T ss_pred HHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHHHHH-HHCCCcEEEEeCC
Confidence 35689999999999877765533 223342 333 345566677 5899999888777
Q ss_pred cCCCC
Q 037419 66 EFSSN 70 (110)
Q Consensus 66 p~~~~ 70 (110)
+..++
T Consensus 146 ~qgps 150 (369)
T PRK11670 146 IYGPS 150 (369)
T ss_pred CCCCC
Confidence 76655
No 59
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=33.53 E-value=70 Score=19.04 Aligned_cols=41 Identities=17% Similarity=0.242 Sum_probs=25.0
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCc
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRR 58 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~ 58 (110)
-.|+.| .++++.|.+. ||.--.+|... + ....+.+ ++.|+.
T Consensus 7 ~~Cp~C-~~ak~~L~~~-~i~~~~~di~~---------~-~~~~~~~-~~~g~~ 47 (72)
T TIGR02194 7 NNCVQC-KMTKKALEEH-GIAFEEINIDE---------Q-PEAIDYV-KAQGFR 47 (72)
T ss_pred CCCHHH-HHHHHHHHHC-CCceEEEECCC---------C-HHHHHHH-HHcCCc
Confidence 469999 7788888874 56544444432 2 2345566 366763
No 60
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=33.32 E-value=49 Score=20.08 Aligned_cols=18 Identities=17% Similarity=0.141 Sum_probs=14.6
Q ss_pred HHHHHHHHhcCCCeeEEE
Q 037419 11 YRKVRRALLDMQELESHL 28 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~ 28 (110)
-..|.+.|++++||.+|.
T Consensus 62 L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 62 LNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp HHHHHHHHCTSTTEEEEE
T ss_pred HHHHHHHHHCCCCeeEEE
Confidence 357888899999998774
No 61
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=33.24 E-value=37 Score=24.32 Aligned_cols=28 Identities=14% Similarity=0.202 Sum_probs=23.5
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCCE
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMCR 35 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~k 35 (110)
+||-.-++..+.+++||.++.+=+..+.
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~ 34 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGY 34 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCC
Confidence 5788889999999999999988776653
No 62
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=33.14 E-value=69 Score=23.31 Aligned_cols=32 Identities=9% Similarity=-0.056 Sum_probs=25.3
Q ss_pred EEEecCCCHHHHHHHHHHhcCCcEEEcccccCC
Q 037419 36 VSVSGNFIPQDLAIKIRKKTNRRVEILEIHEFS 68 (110)
Q Consensus 36 VtV~g~~d~~~I~~~I~~k~G~~a~~~~~~p~~ 68 (110)
+.|+|+-|-..|+.+| ++.|.++..++.++..
T Consensus 110 vLvSgD~DF~~Lv~~l-re~G~~V~v~g~~~~t 141 (160)
T TIGR00288 110 ALVTRDADFLPVINKA-KENGKETIVIGAEPGF 141 (160)
T ss_pred EEEeccHhHHHHHHHH-HHCCCEEEEEeCCCCC
Confidence 4457888999999999 5889999988865533
No 63
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=32.65 E-value=1.4e+02 Score=23.72 Aligned_cols=38 Identities=8% Similarity=-0.031 Sum_probs=28.9
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCC
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~ 57 (110)
..|...+++.+.+++||.++.+- +.++-.+.+++..|+
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~~------------sre~~l~~L~~~lg~ 108 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRFI------------SREEALKELQPWLGF 108 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEEe------------CHHHHHHHHHHHcCc
Confidence 78899999999999999987653 445555566566775
No 64
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=32.15 E-value=49 Score=21.73 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=18.3
Q ss_pred HHHHHHHHHhcCCCeeEEEEec
Q 037419 10 CYRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 10 Ca~kIekaL~~l~GV~~v~vd~ 31 (110)
=...++.++.+++||+++++-.
T Consensus 63 ~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 63 GTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred CcHHHHHHHhccCCCcEEEEEE
Confidence 3467899999999999998753
No 65
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=31.38 E-value=84 Score=18.35 Aligned_cols=28 Identities=11% Similarity=0.297 Sum_probs=20.9
Q ss_pred HHHHHHHHhcCCCeeEEEEeccC-CEEEE
Q 037419 11 YRKVRRALLDMQELESHLIEKKM-CRVSV 38 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~-~kVtV 38 (110)
...+++.|.++|.|.++.+...- +++.|
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r~~P~~l~I 64 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSRRFPNTLEI 64 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEEETTTEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEEeCCCEEEE
Confidence 36788889999999999987532 45554
No 66
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=31.11 E-value=1.1e+02 Score=17.79 Aligned_cols=51 Identities=18% Similarity=0.129 Sum_probs=34.5
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEc
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~ 62 (110)
|+.|+.=.-+++++|.+++.=+.+.+- .........|...+ +..|+.....
T Consensus 6 g~~CP~Pl~~~~~~l~~l~~g~~l~v~-------~d~~~~~~~i~~~~-~~~g~~~~~~ 56 (69)
T cd00291 6 GLPCPLPVLKTKKALEKLKSGEVLEVL-------LDDPGAVEDIPAWA-KETGHEVLEV 56 (69)
T ss_pred CCcCCHHHHHHHHHHhcCCCCCEEEEE-------ecCCcHHHHHHHHH-HHcCCEEEEE
Confidence 788999999999999887532222221 11223578888888 6999986543
No 67
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=30.91 E-value=85 Score=21.12 Aligned_cols=29 Identities=24% Similarity=0.307 Sum_probs=24.2
Q ss_pred EEEecCCCHHHHHHHHHHhcCCcEEEcccc
Q 037419 36 VSVSGNFIPQDLAIKIRKKTNRRVEILEIH 65 (110)
Q Consensus 36 VtV~g~~d~~~I~~~I~~k~G~~a~~~~~~ 65 (110)
+.|+|+-|-..+++.+ ++.|+++.+++..
T Consensus 104 vLvSgD~Df~~~i~~l-r~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGDSDFVPLVERL-RELGKRVIVVGFE 132 (149)
T ss_pred EEEECCccHHHHHHHH-HHcCCEEEEEccC
Confidence 3456788999999999 5889999998886
No 68
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=30.69 E-value=71 Score=20.20 Aligned_cols=21 Identities=10% Similarity=0.126 Sum_probs=17.1
Q ss_pred ccCCEEEEecCCCHHHHHHHH
Q 037419 31 KKMCRVSVSGNFIPQDLAIKI 51 (110)
Q Consensus 31 ~~~~kVtV~g~~d~~~I~~~I 51 (110)
+.+|+++++|.-+++++..++
T Consensus 55 F~sGki~itGaks~~~~~~a~ 75 (86)
T PF00352_consen 55 FSSGKIVITGAKSEEEAKKAI 75 (86)
T ss_dssp ETTSEEEEEEESSHHHHHHHH
T ss_pred EcCCEEEEEecCCHHHHHHHH
Confidence 588999999987777776666
No 69
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=30.30 E-value=92 Score=20.67 Aligned_cols=31 Identities=16% Similarity=0.029 Sum_probs=26.4
Q ss_pred EEEeccCCEEEEecCCCHHHHHHHHHHhcCCc
Q 037419 27 HLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRR 58 (110)
Q Consensus 27 v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~ 58 (110)
+.+|...+.++|...+...+|.+.+ .+.|+.
T Consensus 57 ~~id~~~~~v~v~aG~~~~~l~~~l-~~~g~~ 87 (139)
T PF01565_consen 57 IEIDPENGTVTVGAGVTWGDLYEAL-APRGLM 87 (139)
T ss_dssp EEEETTTTEEEEETTSBHHHHHHHH-HHHTEE
T ss_pred ccccccceeEEEeccccchhccccc-cccccc
Confidence 5678889999999889999999999 577763
No 70
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=29.97 E-value=1.3e+02 Score=18.13 Aligned_cols=50 Identities=12% Similarity=0.001 Sum_probs=35.3
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEE
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
|+.|+.=.-+.+++|.+++.=+.+.| .++.......|...+ +..|+++..
T Consensus 6 G~~CP~Pvi~~kkal~~l~~G~~l~V-------~~d~~~s~~ni~~~~-~~~g~~v~~ 55 (69)
T cd03422 6 GEPCPYPAIATLEALPSLKPGEILEV-------ISDCPQSINNIPIDA-RNHGYKVLA 55 (69)
T ss_pred CCcCCHHHHHHHHHHHcCCCCCEEEE-------EecCchHHHHHHHHH-HHcCCEEEE
Confidence 78899999999999999863222222 112334667788888 699998754
No 71
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=29.84 E-value=81 Score=18.69 Aligned_cols=24 Identities=29% Similarity=0.404 Sum_probs=16.8
Q ss_pred cchhHHHHHHHHHhcCCCeeEEEEec
Q 037419 6 DCNGCYRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 6 ~C~~Ca~kIekaL~~l~GV~~v~vd~ 31 (110)
.|+.| .++++.|.+. ||.-..+|.
T Consensus 10 ~C~~C-~ka~~~L~~~-gi~~~~~di 33 (73)
T cd03027 10 GCEDC-TAVRLFLREK-GLPYVEINI 33 (73)
T ss_pred CChhH-HHHHHHHHHC-CCceEEEEC
Confidence 59999 7888888875 565444444
No 72
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.79 E-value=52 Score=22.12 Aligned_cols=22 Identities=9% Similarity=0.019 Sum_probs=19.5
Q ss_pred hcCCCeeEEEEeccCCEEEEec
Q 037419 19 LDMQELESHLIEKKMCRVSVSG 40 (110)
Q Consensus 19 ~~l~GV~~v~vd~~~~kVtV~g 40 (110)
...||++.+++.+.++++.|++
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 4568999999999999999986
No 73
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=29.60 E-value=66 Score=22.15 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=30.0
Q ss_pred CEEEEecCCCHHHHHHHHHHhcCCcEEEcccccCCCCCCCc-chhhhHHh
Q 037419 34 CRVSVSGNFIPQDLAIKIRKKTNRRVEILEIHEFSSNNNNI-IEGHQEQL 82 (110)
Q Consensus 34 ~kVtV~g~~d~~~I~~~I~~k~G~~a~~~~~~p~~~~~~~~-~~~h~~~~ 82 (110)
.++.|.+.....++++.++++.|..+..+..+.. --.-.+ .++|++++
T Consensus 35 Dr~~v~~~~Tl~~li~~~~~~~~lev~ml~~g~~-~LY~~f~~~~~~~rl 83 (125)
T PF09358_consen 35 DRIEVNGDMTLQELIDYFKEKYGLEVTMLSQGVS-LLYSSFPPPKHKERL 83 (125)
T ss_dssp -EEEEES--BHHHHHHHHHHTTS-EEEEEEETTE-EEEETT-HHHHHHHT
T ss_pred eEEEEcCCCCHHHHHHHHHHHhCceEEEEEeCCE-EEEecCChhhhHHHh
Confidence 5667778788999999998788988887766551 111112 46787765
No 74
>PF07145 PAM2: Ataxin-2 C-terminal region; InterPro: IPR009818 This entry represents a conserved region approximately 250 residues long located towards the C terminus of eukaryotic ataxin-2. Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder []. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death []. Ataxin-2 is predicted to consist of mostly non-globular domains [].; PDB: 3NTW_B 1JH4_B 3KTR_B 3KUJ_B 3KUT_D 3KUS_D 1JGN_B 2RQG_A 2RQH_A.
Probab=29.46 E-value=29 Score=16.42 Aligned_cols=9 Identities=56% Similarity=0.523 Sum_probs=7.2
Q ss_pred ccCCCCCcc
Q 037419 99 ISKQNPCAT 107 (110)
Q Consensus 99 ~~~~~~~~~ 107 (110)
.|.-||||-
T Consensus 3 ~s~LNp~A~ 11 (18)
T PF07145_consen 3 SSKLNPNAP 11 (18)
T ss_dssp SSSSSTTSS
T ss_pred ccccCCCCc
Confidence 578899985
No 75
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=29.45 E-value=60 Score=19.54 Aligned_cols=17 Identities=6% Similarity=0.110 Sum_probs=14.3
Q ss_pred HHHHHHHhcCCCeeEEE
Q 037419 12 RKVRRALLDMQELESHL 28 (110)
Q Consensus 12 ~kIekaL~~l~GV~~v~ 28 (110)
..+.+.|++++||.+|.
T Consensus 52 ~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 52 QTLMPEIRRIDGVEDVK 68 (74)
T ss_pred HHHHHHHhCCCCceEEE
Confidence 56788899999998875
No 76
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=29.39 E-value=1.3e+02 Score=18.02 Aligned_cols=48 Identities=8% Similarity=0.041 Sum_probs=34.7
Q ss_pred cccchhHHHHHHHHHhcCC-C-eeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEE
Q 037419 4 NIDCNGCYRKVRRALLDMQ-E-LESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~-G-V~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
|+.|+.=.-+.+++|.+++ | +-.|.+ +.......|...+ ++.|+++..
T Consensus 6 G~~CP~P~i~~k~~l~~l~~G~~l~V~~---------dd~~s~~di~~~~-~~~g~~~~~ 55 (69)
T cd03423 6 GLRCPEPVMMLHKKVRKMKPGDTLLVLA---------TDPSTTRDIPKFC-TFLGHELLA 55 (69)
T ss_pred CCcCCHHHHHHHHHHHcCCCCCEEEEEe---------CCCchHHHHHHHH-HHcCCEEEE
Confidence 7889999999999999985 2 222222 2334667888888 699998754
No 77
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=29.38 E-value=1.1e+02 Score=28.36 Aligned_cols=46 Identities=20% Similarity=0.171 Sum_probs=35.2
Q ss_pred HHHHHHHHhcCCCeeEEEEecc-CCEEEEe--------cCCCHHHHHHHHHHhcCC
Q 037419 11 YRKVRRALLDMQELESHLIEKK-MCRVSVS--------GNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~-~~kVtV~--------g~~d~~~I~~~I~~k~G~ 57 (110)
+..|+..|.+++||.+|.+--. ...+.|. -..+++++..+|+ ....
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~-~qN~ 211 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIR-AQNV 211 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHH-HhCc
Confidence 4678999999999999998765 5666675 2468899999994 5443
No 78
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=29.16 E-value=76 Score=29.14 Aligned_cols=42 Identities=12% Similarity=0.093 Sum_probs=32.5
Q ss_pred HHHHHHHHhcCCCeeEEEEeccC--CEEEEe--------cCCCHHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKM--CRVSVS--------GNFIPQDLAIKIR 52 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~--~kVtV~--------g~~d~~~I~~~I~ 52 (110)
+.+|++.|.++|||.++..|... ..+.|. -.+++++|.+.++
T Consensus 700 a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~ 751 (1051)
T TIGR00914 700 AEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVA 751 (1051)
T ss_pred HHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 57899999999999999988754 445553 2468889988884
No 79
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=29.10 E-value=46 Score=25.38 Aligned_cols=27 Identities=15% Similarity=0.254 Sum_probs=23.6
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCC
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMC 34 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~ 34 (110)
+||-.-++..+.+++||.++.+=+..+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG 78 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGG 78 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence 588899999999999999999888754
No 80
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=29.06 E-value=51 Score=24.60 Aligned_cols=28 Identities=7% Similarity=0.113 Sum_probs=20.9
Q ss_pred HHHHHHHHhcCCCeeEEE--EeccCCEEEE
Q 037419 11 YRKVRRALLDMQELESHL--IEKKMCRVSV 38 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~--vd~~~~kVtV 38 (110)
+++++..|.++.||.+|+ +.+.++.-.|
T Consensus 63 E~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 63 ENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 578999999999998665 5556655544
No 81
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=28.96 E-value=1e+02 Score=17.19 Aligned_cols=17 Identities=24% Similarity=0.618 Sum_probs=13.4
Q ss_pred ccchhHHHHHHHHHhcCC
Q 037419 5 IDCNGCYRKVRRALLDMQ 22 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~ 22 (110)
-.|+.| .+++..|.+..
T Consensus 8 ~~Cp~C-~~~~~~L~~~~ 24 (72)
T cd02066 8 STCPYC-KRAKRLLESLG 24 (72)
T ss_pred CCCHHH-HHHHHHHHHcC
Confidence 359999 77888888874
No 82
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=28.59 E-value=63 Score=21.94 Aligned_cols=19 Identities=16% Similarity=0.476 Sum_probs=15.9
Q ss_pred ccchhHHHHHHHHHhc--CCC
Q 037419 5 IDCNGCYRKVRRALLD--MQE 23 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~--l~G 23 (110)
..|..||..+++.|.+ ++|
T Consensus 19 ~qC~~cA~Al~~~L~~~gI~G 39 (100)
T PF15643_consen 19 FQCVECASALKQFLKQAGIPG 39 (100)
T ss_pred eehHHHHHHHHHHHHHCCCCc
Confidence 5799999999999975 444
No 83
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=28.57 E-value=1.6e+02 Score=18.99 Aligned_cols=46 Identities=17% Similarity=0.253 Sum_probs=27.2
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcE
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a 59 (110)
-.|+.|. ++++.|.++ ||.-..+|.. ...+..++.+.+.+.+|.+.
T Consensus 16 ~~Cp~C~-~ak~~L~~~-~i~~~~vdid-------~~~~~~~~~~~l~~~tg~~t 61 (99)
T TIGR02189 16 SSCCMCH-VVKRLLLTL-GVNPAVHEID-------KEPAGKDIENALSRLGCSPA 61 (99)
T ss_pred CCCHHHH-HHHHHHHHc-CCCCEEEEcC-------CCccHHHHHHHHHHhcCCCC
Confidence 4699995 788888876 5543333332 22334556666644566643
No 84
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=28.47 E-value=61 Score=25.35 Aligned_cols=21 Identities=14% Similarity=0.167 Sum_probs=16.7
Q ss_pred HHHHHHHHHhcCCCeeEEEEe
Q 037419 10 CYRKVRRALLDMQELESHLIE 30 (110)
Q Consensus 10 Ca~kIekaL~~l~GV~~v~vd 30 (110)
=++.+++.|++++||.+++|.
T Consensus 110 ~eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 110 KEQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHHHHHHHhcCceEEEEEE
Confidence 367899999999998865543
No 85
>TIGR02374 nitri_red_nirB nitrite reductase [NAD(P)H], large subunit.
Probab=28.26 E-value=62 Score=28.74 Aligned_cols=53 Identities=15% Similarity=0.196 Sum_probs=30.3
Q ss_pred CcccccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCC
Q 037419 1 MRINIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 1 lkVgM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~ 57 (110)
.+.+..|++|...|++.|...-+..-..+ +.-+--....+-+++.+.|+ ..+.
T Consensus 442 t~ag~~Cg~C~~~~~~il~~~~~~~~~~~---~~~~c~~~~~~~~~~~~~~~-~~~~ 494 (785)
T TIGR02374 442 TKAGTSCGGCKPLVEQLLRAELNSQYTAS---TPALCECTDFSRDELFEEIQ-ARGF 494 (785)
T ss_pred CCCCCCCcCHHHHHHHHHHHHHhhccccc---cCcccCCcCCCHHHHHHHHH-HcCC
Confidence 36789999999999999975433221111 11111123446667766663 4443
No 86
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=27.44 E-value=70 Score=27.49 Aligned_cols=40 Identities=10% Similarity=0.110 Sum_probs=31.8
Q ss_pred hcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEE
Q 037419 19 LDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 19 ~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
..+.-| +++|.+..+|||+..+...+|++.+ ++.|+....
T Consensus 99 ~~lnkV--v~~dpe~~tvTV~aGirlrQLie~~-~~~GlsL~~ 138 (518)
T KOG4730|consen 99 DKLNKV--VEFDPELKTVTVQAGIRLRQLIEEL-AKLGLSLPN 138 (518)
T ss_pred hhhccc--eeeCchhceEEeccCcCHHHHHHHH-HhcCccccC
Confidence 344444 4668888999999999999999999 699996543
No 87
>TIGR01709 typeII_sec_gspL general secretion pathway protein L. This model represents GspL, protein L of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=27.18 E-value=1.8e+02 Score=23.26 Aligned_cols=49 Identities=12% Similarity=0.064 Sum_probs=32.5
Q ss_pred HHHHHHhcCCCe--eEEEEeccCCEEEEecCC----CHHHHHHHHHHhcCCcEEEcc
Q 037419 13 KVRRALLDMQEL--ESHLIEKKMCRVSVSGNF----IPQDLAIKIRKKTNRRVEILE 63 (110)
Q Consensus 13 kIekaL~~l~GV--~~v~vd~~~~kVtV~g~~----d~~~I~~~I~~k~G~~a~~~~ 63 (110)
.+-.+|...+|+ .++++|-..+.++++... +.+.+...+ + .||.++.-.
T Consensus 314 ~l~~al~~~~~~~l~sL~y~~~~~~L~l~l~a~~~~~le~l~~~l-~-~g~~v~~~~ 368 (384)
T TIGR01709 314 ALATALGQLPGLQLQSLDFDGARGELRLKLEAPSDADLEQLRSRL-A-RGFQVALGQ 368 (384)
T ss_pred HHHHHhccCCCCceeEEeEcCCCCEEEEEEecCChHHHHHHHHHH-h-hhceecccc
Confidence 455666666774 466666667888876432 556777788 6 899887643
No 88
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=27.10 E-value=1.5e+02 Score=17.84 Aligned_cols=48 Identities=19% Similarity=0.264 Sum_probs=34.7
Q ss_pred cccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEe--cCCCHHHHHHHHHHhcCCcEEE
Q 037419 4 NIDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVS--GNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~--g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
|+.|+.=.-+.+++|.+++.=+ .+.|. .......|.... ++.|++...
T Consensus 6 G~~CP~Pvl~~kkal~~l~~G~---------~l~V~~d~~~a~~di~~~~-~~~G~~~~~ 55 (69)
T cd03420 6 GLQCPGPILKLKKEIDKLQDGE---------QLEVKASDPGFARDAQAWC-KSTGNTLIS 55 (69)
T ss_pred CCcCCHHHHHHHHHHHcCCCCC---------EEEEEECCccHHHHHHHHH-HHcCCEEEE
Confidence 7899999999999999986222 22332 234567788888 699997753
No 89
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=26.98 E-value=1.2e+02 Score=21.97 Aligned_cols=30 Identities=3% Similarity=-0.035 Sum_probs=25.4
Q ss_pred hHHHHHHHHHhcCCCeeEEEEeccCCEEEE
Q 037419 9 GCYRKVRRALLDMQELESHLIEKKMCRVSV 38 (110)
Q Consensus 9 ~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV 38 (110)
.=+.+|.+.+.++|||.++.+=.....+.|
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~V 83 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYV 83 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEE
Confidence 346789999999999999998887777776
No 90
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=26.55 E-value=60 Score=21.54 Aligned_cols=21 Identities=24% Similarity=0.305 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCeeEEEEec
Q 037419 11 YRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~ 31 (110)
-..++++|..++||+++++-.
T Consensus 64 td~~ee~l~~vegV~sveve~ 84 (88)
T COG2092 64 TDALEEALEEVEGVESVEVEN 84 (88)
T ss_pred cHHHHHHHhhccCcceEEEEE
Confidence 457899999999999988753
No 91
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=26.47 E-value=1.2e+02 Score=24.49 Aligned_cols=37 Identities=3% Similarity=-0.000 Sum_probs=29.9
Q ss_pred hcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCc
Q 037419 19 LDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRR 58 (110)
Q Consensus 19 ~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~ 58 (110)
.++.+|. ++|....+|+|.......+|.+.+ .+.|+.
T Consensus 44 ~~ln~Il--e~d~~~~~vtV~AG~~l~el~~~L-~~~G~~ 80 (352)
T PRK11282 44 RAHRGIV--SYDPTELVITARAGTPLAELEAAL-AEAGQM 80 (352)
T ss_pred ccCCCcE--EEcCCCCEEEECCCCCHHHHHHHH-HHcCCe
Confidence 4555653 678888999999889999999999 588873
No 92
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=26.27 E-value=1.1e+02 Score=17.11 Aligned_cols=23 Identities=22% Similarity=0.254 Sum_probs=14.2
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEE
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLI 29 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~v 29 (110)
-.|+.|. ++++.|... |+.-..+
T Consensus 8 ~~C~~C~-~~~~~l~~~-~i~~~~v 30 (74)
T TIGR02196 8 PWCPPCK-KAKEYLTSK-GIAFEEI 30 (74)
T ss_pred CCChhHH-HHHHHHHHC-CCeEEEE
Confidence 3599995 567778763 4543333
No 93
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=26.09 E-value=1.6e+02 Score=19.38 Aligned_cols=46 Identities=20% Similarity=0.289 Sum_probs=30.1
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcE
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a 59 (110)
-+|+.| ++.++.|.+. ||.-..+|+.. ...+..++.+.+ ..+|...
T Consensus 7 ~~C~~c-~ka~~~L~~~-~i~~~~idi~~------~~~~~~el~~l~-~~~~~~~ 52 (117)
T TIGR01617 7 PNCTTC-KKARRWLEAN-GIEYQFIDIGE------DGPTREELLDIL-SLLEDGI 52 (117)
T ss_pred CCCHHH-HHHHHHHHHc-CCceEEEecCC------ChhhHHHHHHHH-HHcCCCH
Confidence 469999 5566777764 66655566542 234567888888 5888543
No 94
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=26.05 E-value=79 Score=23.41 Aligned_cols=21 Identities=10% Similarity=0.181 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCeeEEEEec
Q 037419 11 YRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~ 31 (110)
.+.+++.|..++||.+++|.+
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 467889999999999888766
No 95
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=26.00 E-value=97 Score=18.84 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=17.5
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEec
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~ 31 (110)
-.|+.| .++++.|... ||.-..+|+
T Consensus 16 ~~Cp~C-~~ak~~L~~~-gi~y~~idi 40 (79)
T TIGR02190 16 PGCPFC-AKAKATLKEK-GYDFEEIPL 40 (79)
T ss_pred CCCHhH-HHHHHHHHHc-CCCcEEEEC
Confidence 479999 7788888775 565444444
No 96
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=25.96 E-value=1e+02 Score=18.15 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=16.7
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEec
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~ 31 (110)
-.|+.| .+.++.|.+. ||.-..+|.
T Consensus 9 ~~Cp~C-~~ak~~L~~~-~i~~~~~~v 33 (72)
T cd03029 9 PGCPFC-ARAKAALQEN-GISYEEIPL 33 (72)
T ss_pred CCCHHH-HHHHHHHHHc-CCCcEEEEC
Confidence 469999 5668888875 565444444
No 97
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=25.27 E-value=1.4e+02 Score=16.87 Aligned_cols=26 Identities=15% Similarity=0.328 Sum_probs=17.3
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEecc
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEKK 32 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~~ 32 (110)
-.|+.| .+.++.|.+. |+.-..+|+.
T Consensus 7 ~~C~~C-~~~~~~L~~~-~i~y~~~dv~ 32 (60)
T PF00462_consen 7 PGCPYC-KKAKEFLDEK-GIPYEEVDVD 32 (60)
T ss_dssp TTSHHH-HHHHHHHHHT-TBEEEEEEGG
T ss_pred CCCcCH-HHHHHHHHHc-CCeeeEcccc
Confidence 469999 6677778664 5664445544
No 98
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.22 E-value=1.5e+02 Score=17.14 Aligned_cols=51 Identities=16% Similarity=0.034 Sum_probs=30.2
Q ss_pred hhHHHHHHHHHhcCCC-eeEEEEecc----CCEEEEe--cCCCHHHHHHHHHHhcCCcE
Q 037419 8 NGCYRKVRRALLDMQE-LESHLIEKK----MCRVSVS--GNFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~G-V~~v~vd~~----~~kVtV~--g~~d~~~I~~~I~~k~G~~a 59 (110)
+|...+|.+.|.+... +.++..... .+.+.+. ...+.+.+.+.| ++.||++
T Consensus 12 ~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~L-~~~G~~v 69 (69)
T cd04909 12 PGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEIL-KEAGYEV 69 (69)
T ss_pred CCHHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCHHHHHHHHHHH-HHcCCcC
Confidence 4556677788866533 444443332 3334433 223678999999 6999853
No 99
>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases. This model represents a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesizing ascorbic acid or a derivative. These include L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by Prosite motif PS00862; OX2_COVAL_FAD; 1.
Probab=25.21 E-value=1.4e+02 Score=24.71 Aligned_cols=41 Identities=12% Similarity=0.172 Sum_probs=31.2
Q ss_pred cCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEEcc
Q 037419 20 DMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEILE 63 (110)
Q Consensus 20 ~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~~~ 63 (110)
++.+|. .+|..+++|+|.+.+...+|.+.+ .+.|+.....+
T Consensus 65 ~l~~i~--~id~~~~~vtV~aG~~l~~L~~~L-~~~Gl~l~~~g 105 (438)
T TIGR01678 65 KMNKVL--QFDKEKKQITVEAGIRLYQLHEQL-DEHGYSMSNLG 105 (438)
T ss_pred hcCCce--EEcCCCCEEEEcCCCCHHHHHHHH-HHcCCEecCCC
Confidence 445543 577788899999889999999999 59998754333
No 100
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=24.97 E-value=2.1e+02 Score=18.78 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=27.7
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCC
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~ 57 (110)
-.|+.| ++.++.|.+. |+.-..+|+... ..+..+|...+ .++|.
T Consensus 7 ~~C~~c-~ka~~~L~~~-~i~~~~idi~~~------~~~~~el~~~~-~~~~~ 50 (111)
T cd03036 7 PKCSTC-RKAKKWLDEH-GVDYTAIDIVEE------PPSKEELKKWL-EKSGL 50 (111)
T ss_pred CCCHHH-HHHHHHHHHc-CCceEEecccCC------cccHHHHHHHH-HHcCC
Confidence 469999 5566777764 666555665433 23556677667 46664
No 101
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=24.83 E-value=42 Score=25.03 Aligned_cols=28 Identities=14% Similarity=0.211 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCCE
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMCR 35 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~k 35 (110)
+||-.-++..+.+++||.++.+=+..+.
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 5788889999999999999998887764
No 102
>PRK10568 periplasmic protein; Provisional
Probab=24.82 E-value=1.7e+02 Score=21.62 Aligned_cols=35 Identities=23% Similarity=0.270 Sum_probs=27.0
Q ss_pred hHHHHHHHHHhcCCCee--EEEEeccCCEEEEecCCC
Q 037419 9 GCYRKVRRALLDMQELE--SHLIEKKMCRVSVSGNFI 43 (110)
Q Consensus 9 ~Ca~kIekaL~~l~GV~--~v~vd~~~~kVtV~g~~d 43 (110)
.=..+|+.+|..-+++. .+.|...+|.|++.|.++
T Consensus 60 ~I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 60 AITAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred HHHHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 34578888887766654 677888899999999874
No 103
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=24.51 E-value=87 Score=25.05 Aligned_cols=37 Identities=11% Similarity=0.114 Sum_probs=29.8
Q ss_pred cCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcE
Q 037419 20 DMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 20 ~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a 59 (110)
++.+|. ++|..+++++|...+...+|.+.+ ++.|+..
T Consensus 83 ~mn~i~--~id~~~~~~~v~aGv~l~~l~~~l-~~~G~~~ 119 (459)
T COG0277 83 RLNRIL--EIDPEDGTATVQAGVTLEDLEKAL-APHGLFL 119 (459)
T ss_pred hhcchh--ccCcCCCEEEEcCCccHHHHHHHH-HHcCCcc
Confidence 344443 688899999999888999999999 5889844
No 104
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=24.24 E-value=1e+02 Score=17.13 Aligned_cols=17 Identities=12% Similarity=0.047 Sum_probs=13.8
Q ss_pred HHHHHHHhcCCCeeEEE
Q 037419 12 RKVRRALLDMQELESHL 28 (110)
Q Consensus 12 ~kIekaL~~l~GV~~v~ 28 (110)
..+.+.|++++||.++.
T Consensus 53 ~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 53 EEVLEELKALPGIIRVR 69 (71)
T ss_pred HHHHHHHHcCCCeEEEE
Confidence 46788899999998775
No 105
>TIGR01679 bact_FAD_ox FAD-linked oxidoreductase. This model represents a family of bacterial oxidoreductases with covalently linked FAD, closely related to two different eukaryotic oxidases, L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae.
Probab=24.19 E-value=1.4e+02 Score=24.38 Aligned_cols=32 Identities=9% Similarity=0.060 Sum_probs=27.4
Q ss_pred EEeccCCEEEEecCCCHHHHHHHHHHhcCCcEE
Q 037419 28 LIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVE 60 (110)
Q Consensus 28 ~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~ 60 (110)
.+|..+++|+|.+.+...+|.+.+ .+.|+...
T Consensus 65 ~~d~~~~~v~v~aG~~l~~l~~~L-~~~G~~l~ 96 (419)
T TIGR01679 65 DVDQPTGLATVEAGTRLGALGPQL-AQRGLGLE 96 (419)
T ss_pred eecCCCCEEEEcCCCCHHHHHHHH-HHcCCccc
Confidence 678888999999889999999999 59998543
No 106
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=23.88 E-value=2.1e+02 Score=18.36 Aligned_cols=38 Identities=24% Similarity=0.236 Sum_probs=26.9
Q ss_pred HHHHHHhcCCCeeEEEEeccCCEEEEe--cCCCHHHHHHHHH
Q 037419 13 KVRRALLDMQELESHLIEKKMCRVSVS--GNFIPQDLAIKIR 52 (110)
Q Consensus 13 kIekaL~~l~GV~~v~vd~~~~kVtV~--g~~d~~~I~~~I~ 52 (110)
-+-+.|-+++||.+|-+ ..+=|+|+ ..++.+.|...|.
T Consensus 38 pLA~~Lf~i~gV~~Vf~--~~dfItVtK~~~~~W~~l~~~I~ 77 (87)
T PF08712_consen 38 PLAQALFAIPGVKSVFI--GDDFITVTKNPDADWEDLKPEIR 77 (87)
T ss_dssp HHHHHHHTSTTEEEEEE--ETTEEEEEE-TTS-HHHHHHHHH
T ss_pred HHHHHhcCCCCEeEEEE--ECCEEEEeeCCCCCHHHHHHHHH
Confidence 34456669999987654 56778886 5578888888774
No 107
>cd06482 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role.
Probab=23.85 E-value=65 Score=20.83 Aligned_cols=23 Identities=26% Similarity=0.229 Sum_probs=18.7
Q ss_pred cCCCee--EEEEeccCCEEEEecCC
Q 037419 20 DMQELE--SHLIEKKMCRVSVSGNF 42 (110)
Q Consensus 20 ~l~GV~--~v~vd~~~~kVtV~g~~ 42 (110)
.+||+. +++|.+..+.|+|.|.-
T Consensus 15 dlPG~~kedI~V~v~~~~L~I~ger 39 (87)
T cd06482 15 DVCGFEPDQVKVKVKDGKVQVSAER 39 (87)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEEE
Confidence 578876 78888899999998853
No 108
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=23.80 E-value=92 Score=24.25 Aligned_cols=21 Identities=10% Similarity=0.150 Sum_probs=18.3
Q ss_pred HHHHHHHHhcCCCeeEEEEec
Q 037419 11 YRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~ 31 (110)
++.+++.|..++||.+++|.+
T Consensus 109 egELarTI~~idgV~~ArVhL 129 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTI 129 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEE
Confidence 567899999999999888865
No 109
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=23.73 E-value=1.2e+02 Score=17.79 Aligned_cols=28 Identities=25% Similarity=0.270 Sum_probs=16.3
Q ss_pred HHHHHHHhc-----CCCeeEEEEeccCCEEEEe
Q 037419 12 RKVRRALLD-----MQELESHLIEKKMCRVSVS 39 (110)
Q Consensus 12 ~kIekaL~~-----l~GV~~v~vd~~~~kVtV~ 39 (110)
+++++.|.+ ++||..|.+-...+++.+-
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~ 34 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVF 34 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEEE
Confidence 355566654 5789999888888777653
No 110
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=23.73 E-value=80 Score=19.17 Aligned_cols=9 Identities=22% Similarity=0.534 Sum_probs=7.1
Q ss_pred ccccchhHH
Q 037419 3 INIDCNGCY 11 (110)
Q Consensus 3 VgM~C~~Ca 11 (110)
++.+|+.|.
T Consensus 6 ~~~~C~~C~ 14 (76)
T PF13192_consen 6 FSPGCPYCP 14 (76)
T ss_dssp ECSSCTTHH
T ss_pred eCCCCCCcH
Confidence 466799997
No 111
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=23.26 E-value=1.4e+02 Score=27.17 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=34.2
Q ss_pred hHHHHHHHHHhcCCCeeEEEEeccCCEEEEe----------cCCCHHHHHHHHH
Q 037419 9 GCYRKVRRALLDMQELESHLIEKKMCRVSVS----------GNFIPQDLAIKIR 52 (110)
Q Consensus 9 ~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~----------g~~d~~~I~~~I~ 52 (110)
.=+.+|++.|+++||+.++..|+..++-.+. ..+++++|...++
T Consensus 687 ~~a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~ 740 (1021)
T PF00873_consen 687 KAAEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLR 740 (1021)
T ss_dssp HHHHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHH
Confidence 3468899999999999999999988766653 2357888888884
No 112
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=23.13 E-value=2.1e+02 Score=18.26 Aligned_cols=52 Identities=15% Similarity=0.179 Sum_probs=34.8
Q ss_pred hHHHHHHHHHhcCCCeeEEEEeccCCEEEEe----cCCCHHHHHHHHHHhcCCcEEE
Q 037419 9 GCYRKVRRALLDMQELESHLIEKKMCRVSVS----GNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 9 ~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~----g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
-|...++..-..+. +.+++..++.+++++- +.+|--.+++.|.+..+-++++
T Consensus 30 ~c~~~~~~~~L~m~-lvd~e~~~D~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RIem 85 (88)
T PF04468_consen 30 FCRELVKELGLPMK-LVDVEYQFDGSKLTFYYTAESRVDFRELVRDLAREFKTRIEM 85 (88)
T ss_pred HHHHHHHHcCCCeE-EEEEEEEcCCCEEEEEEEeCCcCcHHHHHHHHHHHhCceEEE
Confidence 45555555433332 5578888899999984 4579999999886555554443
No 113
>PF03434 DUF276: DUF276 ; InterPro: IPR005096 This family is specific to Borrelia burgdorferi (Lyme disease spirochete). The protein is encoded on extrachromosomal DNA and is of unknown function.
Probab=23.04 E-value=1.2e+02 Score=23.94 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=24.5
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEE
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSV 38 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV 38 (110)
...|+++|..++||+.+.+--..|++.+
T Consensus 89 y~Avk~aLL~~~gv~haNI~SsaGtini 116 (291)
T PF03434_consen 89 YEAVKSALLNLNGVEHANIKSSAGTINI 116 (291)
T ss_pred HHHHHHHhcCCCCceeeeeecCCCeeEE
Confidence 4679999999999999988888888876
No 114
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=23.01 E-value=2.4e+02 Score=20.88 Aligned_cols=41 Identities=10% Similarity=0.091 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCCee--EEEEeccCCEEEEecCCCHHHHHHHH
Q 037419 11 YRKVRRALLDMQELE--SHLIEKKMCRVSVSGNFIPQDLAIKI 51 (110)
Q Consensus 11 a~kIekaL~~l~GV~--~v~vd~~~~kVtV~g~~d~~~I~~~I 51 (110)
..+|.+++.+.+||. ++..|..-++..++-.-+++.|.+++
T Consensus 18 ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~a~ 60 (178)
T PF07837_consen 18 IEAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAEAA 60 (178)
T ss_dssp HHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHHHH
Confidence 467888999999976 55566666776665322455554444
No 115
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=22.99 E-value=95 Score=20.24 Aligned_cols=21 Identities=14% Similarity=0.185 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCeeEEEEec
Q 037419 11 YRKVRRALLDMQELESHLIEK 31 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~ 31 (110)
...++.++.+.+||+++++..
T Consensus 64 td~lee~i~~~d~VqsveI~~ 84 (88)
T cd00292 64 TDELEEAISEEDGVQSVDVEA 84 (88)
T ss_pred cHHHHHHHhccCCceEEEEEE
Confidence 367889999999999998754
No 116
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=22.96 E-value=62 Score=21.87 Aligned_cols=26 Identities=31% Similarity=0.319 Sum_probs=15.3
Q ss_pred CEEEEecCCCHHHHHHHHHHhcCCcE
Q 037419 34 CRVSVSGNFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 34 ~kVtV~g~~d~~~I~~~I~~k~G~~a 59 (110)
++|-|.|-.++++|..++.+|.|+.-
T Consensus 13 k~VNV~~c~~a~eI~~rvLKKfg~~~ 38 (105)
T PF14847_consen 13 KTVNVSGCFNAQEIKRRVLKKFGLPE 38 (105)
T ss_dssp EEEE--S--HHHHHHHHHHHHHTSS-
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCcc
Confidence 45556677788887766668999865
No 117
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=22.76 E-value=1.6e+02 Score=27.15 Aligned_cols=37 Identities=14% Similarity=0.095 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCCeeEEEEecc-CCEEEEecCCCHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKK-MCRVSVSGNFIPQDLAI 49 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~-~~kVtV~g~~d~~~I~~ 49 (110)
...|+..|.++|||.+|.+.-. ...+.|. +|++++.+
T Consensus 168 ~~~l~~~L~~i~gV~~V~~~G~~~~ei~V~--vd~~kl~~ 205 (1040)
T PRK10503 168 ETRVAQKISQVSGVGLVTLSGGQRPAVRVK--LNAQAIAA 205 (1040)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEE--ECHHHHHH
No 118
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=22.66 E-value=1.2e+02 Score=19.81 Aligned_cols=21 Identities=19% Similarity=0.113 Sum_probs=17.5
Q ss_pred HHHHHHHH-hcCCCeeEEEEec
Q 037419 11 YRKVRRAL-LDMQELESHLIEK 31 (110)
Q Consensus 11 a~kIekaL-~~l~GV~~v~vd~ 31 (110)
...|+.++ ..++||+++++..
T Consensus 64 ~d~lee~i~~~~e~Vqsvei~~ 85 (89)
T PF00736_consen 64 TDDLEEAIESFEEGVQSVEIES 85 (89)
T ss_dssp HHHHHHHHTTCTTTEEEEEEEE
T ss_pred hHHHHHHHHhcCCCccEEEEEE
Confidence 46788999 9999999998753
No 119
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=22.66 E-value=60 Score=24.09 Aligned_cols=28 Identities=14% Similarity=0.195 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEeccCCE
Q 037419 8 NGCYRKVRRALLDMQELESHLIEKKMCR 35 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~GV~~v~vd~~~~k 35 (110)
+||=.=+++.+.+++||.++.+=+..|.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 5788889999999999999988777664
No 120
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=22.56 E-value=1e+02 Score=18.26 Aligned_cols=20 Identities=40% Similarity=0.441 Sum_probs=13.9
Q ss_pred CEEEEecC-CCHHHHHHHHHH
Q 037419 34 CRVSVSGN-FIPQDLAIKIRK 53 (110)
Q Consensus 34 ~kVtV~g~-~d~~~I~~~I~~ 53 (110)
+.|+|.+. .+++++.++|.+
T Consensus 6 G~Isvs~~~~s~~d~~~~la~ 26 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAK 26 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHH
T ss_pred EEEEEccccCCHHHHHHHHHH
Confidence 56777776 578777777753
No 121
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=22.42 E-value=2.1e+02 Score=25.17 Aligned_cols=60 Identities=8% Similarity=0.073 Sum_probs=42.3
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEecC----C--CHHHHHHHHHHhcCCcEEEcccccCCCC
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVSGN----F--IPQDLAIKIRKKTNRRVEILEIHEFSSN 70 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~g~----~--d~~~I~~~I~~k~G~~a~~~~~~p~~~~ 70 (110)
.+.|++.+-+-.||.++.+|..++.|.|... + .--...+.|.+++|+..+++.-.|..+.
T Consensus 78 ~~~I~eivP~ea~i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PPi~S~ 143 (637)
T COG1782 78 RKIILEIVPEEAGITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPPIQSR 143 (637)
T ss_pred HHHHHHhCccccCceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCCCchh
Confidence 4566666666689999999999999999631 1 1122333444799999998877776655
No 122
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=22.41 E-value=88 Score=20.64 Aligned_cols=29 Identities=28% Similarity=0.291 Sum_probs=19.0
Q ss_pred EEEEecCCCHHHHHHHHHHhcCCcEEEccc
Q 037419 35 RVSVSGNFIPQDLAIKIRKKTNRRVEILEI 64 (110)
Q Consensus 35 kVtV~g~~d~~~I~~~I~~k~G~~a~~~~~ 64 (110)
-+.|+|+.|-..+++.+ +..|+++.+++.
T Consensus 99 ivLvSgD~Df~~~v~~l-~~~g~~V~v~~~ 127 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVRKL-RERGKRVIVVGA 127 (146)
T ss_dssp EEEE---GGGHHHHHHH-HHH--EEEEEE-
T ss_pred EEEEECcHHHHHHHHHH-HHcCCEEEEEEe
Confidence 34457888999999999 599999998884
No 123
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=22.07 E-value=2.2e+02 Score=18.15 Aligned_cols=44 Identities=18% Similarity=0.164 Sum_probs=28.4
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCC
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~ 57 (110)
-+|+.| ++.++.|.+. |+.-..+|+.. ...+.+++.+.+ .+.|.
T Consensus 7 ~~C~~c-~ka~~~L~~~-~i~~~~idi~~------~~~~~~~l~~~~-~~~~~ 50 (105)
T cd02977 7 PNCSTS-RKALAWLEEH-GIEYEFIDYLK------EPPTKEELKELL-AKLGL 50 (105)
T ss_pred CCCHHH-HHHHHHHHHc-CCCcEEEeecc------CCCCHHHHHHHH-HhcCC
Confidence 469999 5556777664 66655555542 334677888777 57774
No 124
>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase. This model represents an uncharacterized plant-specific family of FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (EC 1.3.2.3) from higher plants, D-arabinono-1,4-lactone oxidase (EC 1.1.3.37 from Saccharomyces cerevisiae, and L-gulonolactone oxidase (EC 1.1.3.8) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown.
Probab=21.88 E-value=1.7e+02 Score=25.31 Aligned_cols=33 Identities=12% Similarity=0.225 Sum_probs=27.4
Q ss_pred EEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEE
Q 037419 27 HLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVE 60 (110)
Q Consensus 27 v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~ 60 (110)
+++|..+++|+|.+.+...+|.+.+ .+.|+...
T Consensus 92 l~iD~~~~tVtV~AG~~l~~L~~~L-~~~Glal~ 124 (557)
T TIGR01677 92 VAVDATAMTVTVESGMSLRELIVEA-EKAGLALP 124 (557)
T ss_pred EEEeCCCCEEEECCCCcHHHHHHHH-HHcCCEec
Confidence 4677778899999889999999999 69998543
No 125
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=21.82 E-value=2.5e+02 Score=20.50 Aligned_cols=27 Identities=19% Similarity=0.078 Sum_probs=19.7
Q ss_pred EEEEecC---CCHHHHHHHHHHhcCCcEEEc
Q 037419 35 RVSVSGN---FIPQDLAIKIRKKTNRRVEIL 62 (110)
Q Consensus 35 kVtV~g~---~d~~~I~~~I~~k~G~~a~~~ 62 (110)
.+.|.|. .-+..|++.| ++.||+++.+
T Consensus 230 ~fvvVGa~HL~G~~gvl~lL-r~~Gy~V~~v 259 (259)
T PF01963_consen 230 VFVVVGAGHLPGEDGVLDLL-RKKGYTVEPV 259 (259)
T ss_pred EEEEEcchhccchhhHHHHH-HhCCceeecC
Confidence 3444554 2578899999 6999998864
No 126
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.76 E-value=1.8e+02 Score=16.80 Aligned_cols=51 Identities=12% Similarity=0.120 Sum_probs=31.8
Q ss_pred hhHHHHHHHHHhcCCC-eeEEEEecc----CCEEEEec-CCCHHHHHHHHHHhcCCcE
Q 037419 8 NGCYRKVRRALLDMQE-LESHLIEKK----MCRVSVSG-NFIPQDLAIKIRKKTNRRV 59 (110)
Q Consensus 8 ~~Ca~kIekaL~~l~G-V~~v~vd~~----~~kVtV~g-~~d~~~I~~~I~~k~G~~a 59 (110)
++...+|.+.|.+... +.++..... ...+.|.- ..+++.+.+.| ++.||++
T Consensus 12 pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L-~~~G~~v 68 (72)
T cd04883 12 PGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDL-RRAGYEV 68 (72)
T ss_pred CCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHH-HHCCCee
Confidence 4566778888876533 555544332 22344432 24677999999 6999965
No 127
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=21.66 E-value=1.2e+02 Score=27.78 Aligned_cols=42 Identities=17% Similarity=0.135 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCC--EEEEe--------cCCCHHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKMC--RVSVS--------GNFIPQDLAIKIR 52 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~--kVtV~--------g~~d~~~I~~~I~ 52 (110)
+.+|++.|.+.|||.++..|+..+ .+.|. -.+++.+|.+.++
T Consensus 677 a~~i~~~L~~~pgv~~v~~~~~~~~~el~i~id~~ka~~~Gls~~~v~~~l~ 728 (1025)
T PRK10614 677 EPKIRKALAALPELADVNSDQQDKGAEMALTYDRDTMARLGIDVQAANSLLN 728 (1025)
T ss_pred HHHHHHHHhcCCCeEEeecCCCCCCceEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 678999999999999999887654 55553 2468888888885
No 128
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=21.65 E-value=1.1e+02 Score=24.42 Aligned_cols=50 Identities=12% Similarity=0.014 Sum_probs=28.2
Q ss_pred HHHHHHHHhcCCCeeEEEEec--cCCEEEEecCCCHHHHHHHHHHhcCCcEE
Q 037419 11 YRKVRRALLDMQELESHLIEK--KMCRVSVSGNFIPQDLAIKIRKKTNRRVE 60 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~--~~~kVtV~g~~d~~~I~~~I~~k~G~~a~ 60 (110)
..+|..+..+.|+|.=++++. .-.+-.++---||+.++.+.-+-+++-++
T Consensus 20 ie~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~f~~ik~Aae 71 (302)
T COG3643 20 IEKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAAFALIKKAAE 71 (302)
T ss_pred HHHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHHHHHHHHHHH
Confidence 467778888999987555444 33443343223677766655334444333
No 129
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=21.64 E-value=2.6e+02 Score=18.74 Aligned_cols=40 Identities=20% Similarity=0.116 Sum_probs=27.8
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe-cCCCHHHHHHHH
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS-GNFIPQDLAIKI 51 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~-g~~d~~~I~~~I 51 (110)
...|..+|..+||++=..-|.. |++.|. -..+...+.+.+
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~ti 60 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETI 60 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHH
Confidence 4578999999999975555555 676664 334666676666
No 130
>PF02983 Pro_Al_protease: Alpha-lytic protease prodomain; InterPro: IPR004236 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The alpha-lytic protease prodomain is associated with serine peptidases, specifically the alpha-lytic endopeptidases and streptogrisin A, B, C, D and E, which are bacterial enzymes and which belong to MEROPS peptidase subfamily S1A (IPR001316 from INTERPRO). The protease precursor in Gram-negative bacterial proteases may be a general property of extracellular bacterial proteases []. The proteases are encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [, ]. The pro region also acts as a potent inhibitor of the mature enzyme []. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0005576 extracellular region; PDB: 3PRO_C 2PRO_B 4PRO_C.
Probab=21.61 E-value=2e+02 Score=17.27 Aligned_cols=19 Identities=16% Similarity=0.310 Sum_probs=16.6
Q ss_pred CCeeEEEEeccCCEEEEec
Q 037419 22 QELESHLIEKKMCRVSVSG 40 (110)
Q Consensus 22 ~GV~~v~vd~~~~kVtV~g 40 (110)
.++..+-+|..+++|.|..
T Consensus 23 ~~~~~WyvD~~tn~VVV~a 41 (62)
T PF02983_consen 23 VAVTSWYVDPRTNKVVVTA 41 (62)
T ss_dssp GCEEEEEEECCCTEEEEEE
T ss_pred CCcceEEEeCCCCeEEEEE
Confidence 4688999999999999973
No 131
>cd06475 ACD_HspB1_like Alpha crystallin domain (ACD) found in mammalian small (s)heat shock protein (Hsp)-27 (also denoted HspB1 in human) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Hsp27 shows enhanced synthesis in response to stress. It is a molecular chaperone which interacts with a large number of different proteins. It is found in many types of human cells including breast, uterus, cervix, platelets and cancer cells. Hsp27 has diverse cellular functions including, chaperoning, regulation of actin polymerization, keratinocyte differentiation, regulation of inflammatory pathways in keratinocytes, and protection from oxidative stress through modulating glutathione levels. It is also a subunit of AUF1-containing protein complexes. It has been linked to several transduction pathways regulating cellular functions including differentiat
Probab=21.59 E-value=87 Score=19.91 Aligned_cols=22 Identities=18% Similarity=0.391 Sum_probs=17.8
Q ss_pred cCCCee--EEEEeccCCEEEEecC
Q 037419 20 DMQELE--SHLIEKKMCRVSVSGN 41 (110)
Q Consensus 20 ~l~GV~--~v~vd~~~~kVtV~g~ 41 (110)
.+||+. ++.|++..+.++|.|.
T Consensus 17 dlPG~~~edi~V~v~~~~L~I~g~ 40 (86)
T cd06475 17 DVNHFAPEELVVKTKDGVVEITGK 40 (86)
T ss_pred ECCCCCHHHEEEEEECCEEEEEEE
Confidence 468876 7788888899999885
No 132
>TIGR02183 GRXA Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase.
Probab=21.58 E-value=1.3e+02 Score=18.75 Aligned_cols=25 Identities=16% Similarity=0.425 Sum_probs=16.3
Q ss_pred cchhHHHHHHHHHhcC----CCeeEEEEec
Q 037419 6 DCNGCYRKVRRALLDM----QELESHLIEK 31 (110)
Q Consensus 6 ~C~~Ca~kIekaL~~l----~GV~~v~vd~ 31 (110)
+|+.| .++++.|.++ +|+.-..+|.
T Consensus 9 ~Cp~C-~~ak~~L~~~~~~~~~i~~~~idi 37 (86)
T TIGR02183 9 GCPYC-VRAKQLAEKLAIERADFEFRYIDI 37 (86)
T ss_pred CCccH-HHHHHHHHHhCcccCCCcEEEEEC
Confidence 69999 6677888776 2444444443
No 133
>TIGR02180 GRX_euk Glutaredoxin. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses.
Probab=21.28 E-value=1.9e+02 Score=16.97 Aligned_cols=46 Identities=13% Similarity=0.200 Sum_probs=24.6
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCC
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNR 57 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~ 57 (110)
-.|+.| .++++.|.++. +.. .-..+.|...-+...+.+.+.+..|.
T Consensus 7 ~~Cp~C-~~~~~~L~~~~-i~~-----~~~~~~v~~~~~~~~~~~~l~~~~g~ 52 (84)
T TIGR02180 7 SYCPYC-KKAKEILAKLN-VKP-----AYEVVELDQLSNGSEIQDYLEEITGQ 52 (84)
T ss_pred CCChhH-HHHHHHHHHcC-CCC-----CCEEEEeeCCCChHHHHHHHHHHhCC
Confidence 369999 67778888864 321 01122222222455666666445554
No 134
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=21.27 E-value=1.6e+02 Score=17.05 Aligned_cols=24 Identities=17% Similarity=0.343 Sum_probs=15.9
Q ss_pred ccchhHHHHHHHHHhcCCCeeEEEEe
Q 037419 5 IDCNGCYRKVRRALLDMQELESHLIE 30 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~~v~vd 30 (110)
-.|+.| .++++.|.+. |+.--.+|
T Consensus 8 ~~Cp~C-~~ak~~L~~~-~i~~~~i~ 31 (75)
T cd03418 8 PNCPYC-VRAKALLDKK-GVDYEEID 31 (75)
T ss_pred CCChHH-HHHHHHHHHC-CCcEEEEE
Confidence 369999 6678888875 56433333
No 135
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=21.18 E-value=74 Score=20.20 Aligned_cols=19 Identities=16% Similarity=0.459 Sum_probs=16.3
Q ss_pred cccchhHHHHHHHHHhcCC
Q 037419 4 NIDCNGCYRKVRRALLDMQ 22 (110)
Q Consensus 4 gM~C~~Ca~kIekaL~~l~ 22 (110)
.|.|+.|...-++++++-.
T Consensus 15 tLPC~~Cr~HA~~ai~kNN 33 (70)
T PF04805_consen 15 TLPCPECRIHAKEAIQKNN 33 (70)
T ss_pred cCCCHHHHHHHHHHHHhcC
Confidence 4789999999999998754
No 136
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=20.43 E-value=1.6e+02 Score=16.89 Aligned_cols=19 Identities=21% Similarity=0.373 Sum_probs=13.6
Q ss_pred ccchhHHHHHHHHHhcCCCee
Q 037419 5 IDCNGCYRKVRRALLDMQELE 25 (110)
Q Consensus 5 M~C~~Ca~kIekaL~~l~GV~ 25 (110)
-.|+.| .+++..|.++ |+.
T Consensus 8 ~~C~~C-~~~~~~L~~~-~~~ 26 (77)
T TIGR02200 8 TWCGYC-AQLMRTLDKL-GAA 26 (77)
T ss_pred CCChhH-HHHHHHHHHc-CCc
Confidence 469999 5678888776 444
No 137
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=20.19 E-value=2.9e+02 Score=18.84 Aligned_cols=40 Identities=10% Similarity=0.141 Sum_probs=29.8
Q ss_pred cCCCeeEEEEeccCCEEEEecCCCHHHHHHHHHHhcCCcEEE
Q 037419 20 DMQELESHLIEKKMCRVSVSGNFIPQDLAIKIRKKTNRRVEI 61 (110)
Q Consensus 20 ~l~GV~~v~vd~~~~kVtV~g~~d~~~I~~~I~~k~G~~a~~ 61 (110)
+..|+...++. ..|.+.|.|.--++++++.+ ...|..+..
T Consensus 39 Rt~GirqfEi~-n~G~~RI~gYk~se~~~~~f-~slG~~~K~ 78 (103)
T PF09158_consen 39 RTKGIRQFEIR-NKGEFRIFGYKMSEEIIKKF-TSLGMEVKQ 78 (103)
T ss_dssp EETTEEEEEEE-TTSEEEEEEES--HHHHHHH-HHTT-EEEE
T ss_pred ccCceeEEEEe-cCCcEEEEEEcCCHHHHHHH-HhcCcEEEE
Confidence 45788888874 67888888877788889999 699998776
No 138
>cd06471 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic me
Probab=20.15 E-value=89 Score=19.61 Aligned_cols=23 Identities=13% Similarity=0.182 Sum_probs=18.0
Q ss_pred cCCCee--EEEEeccCCEEEEecCC
Q 037419 20 DMQELE--SHLIEKKMCRVSVSGNF 42 (110)
Q Consensus 20 ~l~GV~--~v~vd~~~~kVtV~g~~ 42 (110)
.||||. ++++.+..+.++|.|.-
T Consensus 17 ~lPGv~~edi~v~~~~~~L~I~g~~ 41 (93)
T cd06471 17 DLPGFKKEDIKLDYKDGYLTISAKR 41 (93)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEEE
Confidence 578874 78888888999998753
No 139
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=20.11 E-value=3.2e+02 Score=24.98 Aligned_cols=29 Identities=10% Similarity=0.133 Sum_probs=23.7
Q ss_pred HHHHHHHHhcCCCeeEEEEeccCCEEEEe
Q 037419 11 YRKVRRALLDMQELESHLIEKKMCRVSVS 39 (110)
Q Consensus 11 a~kIekaL~~l~GV~~v~vd~~~~kVtV~ 39 (110)
...+|++|..++||..+.-.-..+...|.
T Consensus 62 t~plE~~l~~v~gv~~i~S~s~~g~s~i~ 90 (1021)
T PF00873_consen 62 TKPLEEALSSVEGVKEIRSTSREGSSSIT 90 (1021)
T ss_dssp HHHHHHTHCSSTTEEEEEEEETTSEEEEE
T ss_pred HHHHHHHHcCCCCeEEEEEEecCCcEEEE
Confidence 36799999999999999877777766653
Done!